Repetition is a weak spot of the ID anyway; it does not really keep record of the entire game history as a list of 'position signatures' with which it could easily compare the current position. It is aware of the two last-played half-moves, though, and uses those to determine which natural continuations it should still search near the end of its search tree. What it does now is give a slight penalty for moving the same piece as two half-moves earlier, and reduce positive scores by a factor 50% if such a move goes also back to the square it came from, and the earlier one was't a capture. (Even though this might not cause a repetition, it would allow the opponent to reach one if he wants too, and should thus be considered a draw offer.)
In the normal case the shortest repeat loop has 4 half-moves, and requires moving pieces back and forth. So this is what the ID tries to detect in the way described above. In the conquer case repeats can already occur after 2 half-moves, and are brought about by doing the same move instead of the reverse one. So this escapes detection, and fatally interferes with its search strategy to always search moves that recapture to the same square. (Which can go on forever, and then crashes the program.)
Note that the ID never announces a draw by repetition. It only uses the information during its search, to make it aware that certain sequences of moves will not make any progress, and would not be able to convert any advantage that it thinks it has into a win. So that the side that is ahead would avoid these sequences, even if they are the only ones that preserve the advantage it imagines it has. E.g. if you are a Queen ahead, but can only escape perpetual check by sacrificing a Rook, it should not prefer the perpetual just to hang on to the Rook. OTOH, if it is a Rook ahead, and can only escape the perpetual by sacrificing a Queen, it would be preferable to opt for the perpetual; the alternative would likely make you lose. If the repetion would have been forbidden, rather than discouraged by giving it a draw score, it would have no choice but sacrificing the Queen, and lose. So this is not a good idea, unless the rules really are such that repeats are forbidden.
Repetition is a weak spot of the ID anyway; it does not really keep record of the entire game history as a list of 'position signatures' with which it could easily compare the current position. It is aware of the two last-played half-moves, though, and uses those to determine which natural continuations it should still search near the end of its search tree. What it does now is give a slight penalty for moving the same piece as two half-moves earlier, and reduce positive scores by a factor 50% if such a move goes also back to the square it came from, and the earlier one was't a capture. (Even though this might not cause a repetition, it would allow the opponent to reach one if he wants too, and should thus be considered a draw offer.)
In the normal case the shortest repeat loop has 4 half-moves, and requires moving pieces back and forth. So this is what the ID tries to detect in the way described above. In the conquer case repeats can already occur after 2 half-moves, and are brought about by doing the same move instead of the reverse one. So this escapes detection, and fatally interferes with its search strategy to always search moves that recapture to the same square. (Which can go on forever, and then crashes the program.)
Note that the ID never announces a draw by repetition. It only uses the information during its search, to make it aware that certain sequences of moves will not make any progress, and would not be able to convert any advantage that it thinks it has into a win. So that the side that is ahead would avoid these sequences, even if they are the only ones that preserve the advantage it imagines it has. E.g. if you are a Queen ahead, but can only escape perpetual check by sacrificing a Rook, it should not prefer the perpetual just to hang on to the Rook. OTOH, if it is a Rook ahead, and can only escape the perpetual by sacrificing a Queen, it would be preferable to opt for the perpetual; the alternative would likely make you lose. If the repetion would have been forbidden, rather than discouraged by giving it a draw score, it would have no choice but sacrificing the Queen, and lose. So this is not a good idea, unless the rules really are such that repeats are forbidden.