I haven't seen a timeout issue, that I know of. Using it as I described, I don't think that would be an issue. The clip on the TD Is pretty big so it seems to slide pretty easily over knots, swivels, etc. Just make sure it won't slide over a spoon or whatever you have on the end of the line! I almost lost it last year ... just caught the hooks on the spoon!
I haven't tried it with heavy fleas. I did try it on copper (300) and dipseys last fall on Lake O and didn't have any issues. I use it all the time on Champlain for checking temp at depth. I hook it to a downrigger and let it down to the bottom and then retrieve it to find the temp break. I wouldn't hook it anything and leave it out, though. It will mess with the dive rate.
Fishmaster : You let the cores out as far as you want first, then hook the TD to the line and let it slide down. That way you don't have to worry about how long it takes to get the lines out.
Good luck!