Lek I am not sure if anyone told you this or not, but be sure to put your new tape on the take up side (the right side) "upside down" when you first get it and rewind it on the the supply side (the left side). After the tape has finished, then flip the reel so that you will get a true "tails out" recording. I didn't recall seeing this flipping through earlier posts.
Also, there are two speeds that the machine can be set to operate in the library wind mode. Most likely the ATR folks set it up for faster operation which runs I believe at 5 times playback speed. Also, how much of a rebuild did they do? I wouldn't worry about the machine blowing up if you leave it on all the time but according to them, the machine does not need much stabilizing time after you turn it on. This as compared to an older studer 2" - that should be left on all the time.
As a general practice, I leave mine on when I am doing a stretch of mix days and off when it won't be used for days. My electricity bill has shot up quite a bit over the past few months, so it helps with that if nothing else.
As someone said, never leave your masters on the machine unattended. The machine shouldn't ever freak but if it does you can have squid-fettuccine salad where you had music. My machine ate my MRL once before the transport cards were recapped and the power transistors had been replaced and upped. It ate my finger tip too while I watched in horror as it started to munch the tape. Its funny, intelligence would tell you not to try to stop the deck with your hands with something that goes that fast. $300 says, "NOOOOO" and you do it anyway. Or you just do it once.
Have fun learning about tape. Once you get in the groove with it you will never be more happy than when you listen back to the repro heads of your mix. I just finished a remix session a few moments ago -> 15ips, IEC1, +6, 456. Damn good way to hear rock.
Best,
joshua
EDIT: Which heads do you have on your machine? Stock ferrite or Flux Magnetics Extended response heads? I ask becauase that is going to affect your bias. Make sure you know.