Sorry I didn't answer earlier, was away from science for a while.
I've just gave my first tests to your new version of SPMF, and I'm very grateful that you've added maxgap parameter!
Both problems seem to be solved now. Hovever I've found something strange in another algo,
VGEN.
Here's my data.0 -1 0 -1 2 -1 4 -1 5 -1 7 -1 8 -1 9 -1 0 -1 11 -1 1 -1 6 -1 31 -1 32 -1 33 -1 26 -1 33 -1 26 -1 33 -1 26 -1 34 -1 35 -1 36 -1 37 -1 0 -1 26 -1 -2
0 -1 0 -1 2 -1 4 -1 5 -1 7 -1 8 -1 9 -1 0 -1 11 -1 1 -1 6 -1 25 -1 26 -1 25 -1 26 -1 31 -1 38 -1 32 -1 25 -1 26 -1 39 -1 34 -1 35 -1 36 -1 37 -1 0 -1 26 -1 -2
0 -1 1 -1 2 -1 3 -1 4 -1 5 -1 6 -1 0 -1 7 -1 8 -1 9 -1 10 -1 0 -1 11 -1 1 -1 6 -1 0 -1 14 -1 40 -1 41 -1 42 -1 14 -1 0 -1 32 -1 -2
Params:support 1
maxgap 3
Result on VGEN:SUP 3
(no patterns in the output, but the support is there)
I've also noticed that the statistics for this experiment state: "minsup 3", it probably meant "maxgap 3"

Tried it with significantly bigger dataset, the program freeze.