Hm. Okay, ignore almost everything I've written so far. I've had a few errors from other sources, which I found after using @outputmode 2. I switched how I was using my autopattr (I used to use physical connections, now I just let it pick up all named objects) and it was picking up a corrupted object. That was interfering with a lot of things. I also made a series of very elementary mistakes while working on fixing this, which made it much harder.
Second, I thought I had a solution, and it turns out I didn't. And as ^^Spectro^^ just pointed out, my assumptions on some things were terribly wrong.
The origin of my specific problem has to do with the loading of the program after reboot. The settings in the pattrstorage are loaded by a loadbang. I had the actual recall of the presets on a delay of 2 seconds, to give the software time to load (it isn't particularly large, either). After rebooting, the first time you launch a program, it takes longer to load. I set the loadbang on a 30 second delay this time, and it worked fine!
It seems as if the loadbang was executing before the patcher had the ability to do all of it's functions. Is there any other way to go around this? I would like to reduce the timer, but I am hesitant, since my users may have varying system speeds, and it may take longer for them to launch, in which case, it would lose the proper loading, which actually defeats the whole purpose of the program.