Probably I found the problem... I tested both .srt and converted .sup subtitles with TSmuxeR, and even there many of them lasts less than a second; so the problem doesn't lie into the .sup converted files, but in the original .srt.
I checked the "guilty" subtitles, and discovered they are spaced at 35ms from the others; I guess I should increase the "distance" of them, maybe at 50ms or even more... I'll test further, and almost surely I'll release it tomorrow...