Noticed a little bug today. If you use a colon in a process name (e.g. 1: Bottom Layer), you will lose that process when you reopen the file. I tried a number of other characters ();.- and all of them work fine so it's just the colon as far as I can tell although it's probably worth doing a more extensive test.
What OS are you running? I just tried it in Mac and I got colon names to show, although i didnt change any settings in the process just hit add process and changed the name