I know that ideally I should try to break up long scripts into smaller components, and I plan on doing that, but for now I have once more reached around 3000 lines in one script and usually that is no problem but for some reason the debugging on this one is incredibly slow. Writing is delayed at times by seconds which is a bit of a nuisance. The problem persists even if the program has not been run which made me think that software could be the problem. I tried updating from 2012b to 2013a thinking that the problem would be resolved but it hasn't been so far.
Any suggestions? (apart from breaking up the script into smaller pieces of course).