No, that's not really it. The cue thing I mean.

Sometimes when I load a softsub I have to stop/start the movie anyway, the timing will be off occasionally. In some rare cases the sub will not load at all. After stop/starting the subs will usually load instantly when jumping to different parts of the movie/episode I'm watching.

Anyways, thanks for the help, I'm on episode 5 now.

Edit:
Win7 ultimate on my laptop and htpc, htpc is AMD A8-3850, Laptop is E350. Had the same issue on my old ehmmmm.... think it was AMD Athlon 64 X2 5000+

Find it hard to believe if it's cpu related though.