The problem is located at "output/vcd.c" and is the following: in the preamble (ln 148) every channel gets a sign, starting at !, ", #, $, and so on - even if the channel is not activated. therefore channel 2 is alway ", doesn't matter if channel 1 is activated or not. on the other hand, at ln 224, the output starts at the first _activated_ channel, which becomes !, and the next _activated_ is ", and so on...
I guess replacing ln 224 by
g_string_append_c(*out, '!' + index);
should fix the problem
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