Here is another issue regarding ponder:
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Monolith 2 > info depth 24 seldepth 26 currmove a7a6 currmovenumber 14
Houdini 6.03 Pro > info time 88001 nodes 143231320 nps 1627000 tbhits 0 hashfull 477
Monolith 2 > info depth 24 seldepth 26 currmove e7e5 currmovenumber 15
Houdini 6.03 Pro > info time 89002 nodes 144806163 nps 1626000 tbhits 0 hashfull 478
Monolith 2 > info depth 24 seldepth 26 currmove g7g6 currmovenumber 16
Monolith 2 > info depth 24 seldepth 26 currmove f7f5 currmovenumber 17
Houdini 6.03 Pro > info multipv 1 depth 25 seldepth 49 score cp 14 lowerbound time 89135 nodes 145021557 nps 1626000 tbhits 0 hashfull 479 pv e1f3
Houdini 6.03 Pro > info multipv 1 depth 25 seldepth 49 score cp 14 lowerbound time 89135 nodes 145021557 nps 1626000 tbhits 0 hashfull 479 pv e1f3
Houdini 6.03 Pro > info depth 26
Houdini 6.03 Pro > info currmove e1f3 currmovenumber 1
Monolith 2 > info depth 24 seldepth 26 currmove f7f6 currmovenumber 18
Monolith 2 > info depth 24 seldepth 26 currmove d8c6 currmovenumber 19
Monolith 2 > info depth 24 seldepth 26 currmove g7g5 currmovenumber 20
Monolith 2 > info depth 24 seldepth 26 score cp -14 time 89287 nodes 84739697 nps 949070 hashfull 73 tbhits 0 pv c7c5 b2b3 b7b6 e1f3 e8f6 h2h4 d8e6 d2d4 c5d4 f3d4 f8d8 d4f5 g8f8 g2g3 d7d5 c4d5 a8d5 d1e3 d5a5 c1b2 c8b7 f2f3 h7h5 b1c2 b8c7 f1c1
Monolith 2 > bestmove c7c5 ponder b2b3
Monolith 2 < position fen qbbnnrkr/pppppppp/8/8/8/8/PPPPPPPP/QBBNNRKR w HFhf - 0 1 moves c2c4 c7c5 b2b3
Monolith 2 < go ponder wtime 1680899 btime 1710710 winc 5000 binc 5000
Houdini 6.03 Pro < ponderhit
Houdini 6.03 Pro > info multipv 1 depth 25 seldepth 49 score cp 14 time 89290 nodes 145278205 nps 1627000 tbhits 0 hashfull 479 pv e1f3
Houdini 6.03 Pro > info multipv 1 depth 25 seldepth 49 score cp 14 time 89290 nodes 145278205 nps 1627000 tbhits 0 hashfull 479 pv e1f3
Houdini 6.03 Pro > bestmove e1f3 ponder b7b6
Houdini 6.03 Pro < position fen qbbnnrkr/pppppppp/8/8/8/8/PPPPPPPP/QBBNNRKR w HFhf - 0 1 moves c2c4 c7c5 e1f3 b7b6
Houdini 6.03 Pro < go ponder wtime 1680889 btime 1715710 winc 5000 binc 5000
Monolith 2 < stop
Monolith 2 > bestmove 0000
Houdini 6.03 Pro > info multipv 1 depth 16 seldepth 32 score cp 22 time 133 nodes 288387 nps 2168000 tbhits 0 pv b2b4 c5b4 a2a3 b8d6 d1e3 e7e6 a3b4 d6b4 h2h4 c8b7 d2d4 a7a5 c1b2 b7f3 e2f3 f7f5
Houdini 6.03 Pro > info multipv 1 depth 17 seldepth 34 score cp 24 time 243 nodes 506739 nps 2085000 tbhits 0 pv b2b4 c5b4 a2a3 b8d6 d1e3 e7e6 a3b4 d6b4 h2h4 c8b7 d2d4 f7f5 h4h5 a7a5 h5h6 b7f3 e2f3 f8f6 h6g7 e8g7 h1h3
Houdini 6.03 Pro > info multipv 1 depth 18 seldepth 37 score cp 25 time 852 nodes 1558139 nps 1828000 tbhits 0 pv b2b4 c5b4 a2a3 b4b3 a1c3 e7e6 c3b3 f7f5 d2d4 e8f6 d1c3 c8a6 c1d2 d8f7 b1d3 f8c8 f1c1 g8h8
Houdini 6.03 Pro > info time 1003 nodes 1801802 nps 1796000 tbhits 0 hashfull 479
Houdini 6.03 Pro > info multipv 1 depth 19 seldepth 37 score cp 21 time 1362 nodes 2400186 nps 1762000 tbhits 0 hashfull 480 pv b2b4 c5b4 a2a3 b4b3 a1c3 e7e6 c3b3 f7f5 h2h4 e8f6 h1h3 f8e8 d2d4 g8h8 d1c3 d8f7 c1g5 c8b7 g5f6
Houdini 6.03 Pro > info depth 20
Houdini 6.03 Pro > info time 2003 nodes 3558619 nps 1776000 tbhits 0 hashfull 483
Houdini 6.03 Pro > info time 3003 nodes 5168122 nps 1720000 tbhits 0 hashfull 484
Houdini 6.03 Pro > info multipv 1 depth 20 seldepth 40 score cp 18 time 3334 nodes 5736330 nps 1720000 tbhits 0 hashfull 485 pv b2b4 c5b4 a2a3 b4b3 a1c3 e7e6 c3b3 d8c6 d2d4 f7f5 c1d2 c8a6 d1e3 e8f6 d4d5 c6a5 d2a5 b6a5 d5e6 d7e6 c4c5 f6d5 e3d5
Houdini 6.03 Pro > info depth 21
Houdini 6.03 Pro > info time 4003 nodes 6866819 nps 1715000 tbhits 0 hashfull 487
Houdini 6.03 Pro > info multipv 1 depth 21 seldepth 40 score cp 18 upperbound time 4051 nodes 6949486 nps 1715000 tbhits 0 hashfull 487 pv b2b4 c5b4
Houdini 6.03 Pro > info currmove a2a3 currmovenumber 2
Houdini 6.03 Pro > info currmove b1f5 currmovenumber 3
Houdini 6.03 Pro > info currmove e2e4 currmovenumber 4
Houdini 6.03 Pro > info currmove d2d4 currmovenumber 5
Houdini 6.03 Pro > info currmove d1c3 currmovenumber 6
Houdini 6.03 Pro > info currmove d2d3 currmovenumber 7
Houdini 6.03 Pro > info currmove f1e1 currmovenumber 8
Houdini 6.03 Pro > info currmove f3e5 currmovenumber 9
Houdini 6.03 Pro > info currmove b1d3 currmovenumber 10
Houdini 6.03 Pro > info currmove g2g3 currmovenumber 11
Houdini 6.03 Pro > info currmove f3d4 currmovenumber 12
Houdini 6.03 Pro > info currmove h2h4 currmovenumber 13
Houdini 6.03 Pro > info currmove b1e4 currmovenumber 14
Houdini 6.03 Pro > info currmove b1c2 currmovenumber 15
Houdini 6.03 Pro > info currmove e2e3 currmovenumber 16
Houdini 6.03 Pro > info currmove d1e3 currmovenumber 17
Houdini 6.03 Pro > info currmove f3g5 currmovenumber 18
Houdini 6.03 Pro > info currmove h2h3 currmovenumber 19
Houdini 6.03 Pro > info currmove a2a4 currmovenumber 20
Houdini 6.03 Pro > info currmove b2b3 currmovenumber 21
Houdini 6.03 Pro > info currmove f3h4 currmovenumber 22
Houdini 6.03 Pro > info currmove f3e1 currmovenumber 23
Houdini 6.03 Pro > info currmove g2g4 currmovenumber 24
Houdini 6.03 Pro > info currmove b1g6 currmovenumber 25
Houdini 6.03 Pro > info currmove b1h7 currmovenumber 26
Houdini 6.03 Pro > info currmove b2b4 currmovenumber 1
You will see in the logs that it's Monolith's time to move, and it's thinking, while Houdini is pondering. Then Monolith stops thinking and plays a move
Monolith 2 > bestmove c7c5 ponder b2b3
So Banksia feeds it the new position and tells it to go ponder on that move b2b3
Monolith 2 < position fen qbbnnrkr/pppppppp/8/8/8/8/PPPPPPPP/QBBNNRKR w HFhf - 0 1 moves c2c4 c7c5 b2b3
Monolith 2 < go ponder wtime 1680899 btime 1710710 winc 5000 binc 5000
Then, as Houdini guessed Monolith's move, it's given the ponderhit command, so far so good
Houdini 6.03 Pro < ponderhit
Houdini quickly plays a move and Banksia gives it the new position and tells it to go ponder on a new move
Houdini 6.03 Pro > bestmove e1f3 ponder b7b6
Houdini 6.03 Pro < position fen qbbnnrkr/pppppppp/8/8/8/8/PPPPPPPP/QBBNNRKR w HFhf - 0 1 moves c2c4 c7c5 e1f3 b7b6
Houdini 6.03 Pro < go ponder wtime 1680889 btime 1715710 winc 5000 binc 5000
Then Banksia tells Monolith to stop, to which monolith answers with bestmove 0000, and then nothing else happens. Banksia never gives Monolith the correct move to search, and eventually Monolith loses on time, as it never starts thinking
Monolith 2 < stop
Monolith 2 > bestmove 0000
I've seen this happen with Ethereal and Minic also.