Strange behavour using linux

Hello,

Because im on a 32 bits windows machine, and rather not use my laptop for programming I decided to install Linux Mint 64 "As a partition" and Quartus 14.0.

This works! Alhough it seems to work. But there is one strange thing going on..

Whenever I use the programmer to program via USB, a lot of unplanned LEDS seem to sort of barely light up in the process. Nevertheless it performs its function of using the (megafunction) pll to count through its steps, and the buttons work as well. But it doesnt really feel safe. Also the Leds that are connected are seemingly performing better, more contrast so to say..

Any pointers?