Theoretically, it should make no difference if the program is started from the StartUp folder or from the Run key. In my opinion, in the StartUp folder it would only confuse some users, and besides that, as you say, some users may e.g. disable it by mistake...
If there is a difference between those 2 startup methods, there is a problem with the order of the application startup (the order is probably changed when you move avast from the Run key to the StartUp folder). However, Windows are not a deterministic system - the order of the application startup is (can be) different on each boot anyway. I.e. even when you say it works now, when you moved avast to the StartUp folder, I don't think it's 100% reliable. Besides, for other users it might work with the Run key, and cause problems when in Startup folder.
Could you try e.g. to temporarily disable the other startup items (and keep avast as it was)? Maybe you'd find what is causing the conflict... And maybe try some more exhaustive "startup dump" (there are many more keys, similar to the "Run" one).
To make myself clear: your method is certainly a nice trick. If there is a conflict, however, we would like to find out what the conflict is and fix it "properly".