excellent, thanks a lot for finding out more about this.
I could narrow it down to this:
xa=0
xb=0
On reload, it’ll become xa=11. I think I know what’s happening: you can also specify numbers using hex notation, like xa=0x7F.
Upon reading such a file, the Rules are following one another, so it will read like this:
xa=0xb=0
And 0xb is hexadecimal for 11.
It’s fun being a detective 
So for now, an easy workaround is to not assign 0, but, for example, another 0 variable. But also to avoid other occurrences of a 0->newline->x.
pp=0
// avoid 0 newline x
pp=pp
xa=pp
xb=pp
(...)
However, the last question is: why do you want to zero out all variables? Upon start of the project, all global variables are guaranteed to be zero. If you want to restart your project at any given time, use the Execute File outgoing action with just the project filename (including .bmtp extension) as filename (no path necessary):
When triggered, the outgoing action will cause a reload of the project file and initialize all global variables to zero.
I’ll report here when this bug is fixed.