do you think i should re-download it maybe? i could take the save and screenshots files and then once i re-download the game, i put them back in. also, maybe the skipping function affects the game performance?
The safest thing would be to download it and copy your save files and such over to the new folder so you have the old folder as a backup. Any saves from v1.3.1 should work fine in v1.3, and vice-versa, since the only difference is in how the game data is handled while the game runs.
If you by skipping mean holding down to double the cutscene speed, then that should only make the game skip every 2 frames, which should only affect performance in places where a lot of new data is being handled, and then that also depends on how strong your PC is I think.
I have the exact same problem. I have Bonds 1.3.1 from DLSite and it keeps progressively getting slower and slower in Session mode, until it takes literally seconds to react per click. Only completely quitting and relaunching the game fixes it. This is a quad-core x64 CPU with 16GB RAM mind you, so really, this is not about the hardware. And I don't remember having this problem at all in 1.2...