It's been a rule of thumb in software sequencers ever since there were software sequencers that it's been a bad idea to put any MIDI notes or audio on beat one, bar one because it's asking for exactly the problem you have found. Some people recommend leaving one bar, others two, others recommend more. I often use 8, but that's so I can shove an intro in later if I want to :-)
It requires an amount of time, however short, for any DAW to check MIDI and audio sync plus handle the other stuff it sends at the start of a project - program/bank changes, controllers, MIDI Start, whatever. Asking for a note-on to be accurately sent on the first MIDI click of the project as well as all this stuff is a bit optimistic.
If you've got away with it before, you've been lucky.
The PC in my sig is pretty powerful, but I wouldn't expect it to reliably start playing a project with a MIDI note on beat 1/bar 1. It might, if it's a very simple project, but once the data builds up it gets less and less likely.