Been botting 8 hours a day for the last three weeks and never seen the game skip a second in the middle of a mission. I only have it skip during the first two seconds of a mission. What happens regularly though is that SWTOR changes the fonts very slightly. Different brightness, different character width, different spacing between characters. Hard for the human eye to notice because it's only a pixel and very subtle brightness shifts, but enough to throw off most bots. The really annoying part is that you can't just crank up shade variation, because when doing so the bot will sooner or later start confusing an 8 with a 9, 6, 5 or 3 or even 0.
Even more annoying is the fact that the French mission timer has again a different character spacing than the English mission timer. Haven't checked the German mission timer yet.
What we could really use is the memory address at which the mission time is found, and perhaps a word from the cracks on whether or not reading the game's memory will get you on SWTOR's anticheat's radar. Unfortunately I know jack shit about reversing.