Oh! Mmm.. I have an idea here..

The point where Hijack EXECs GPSapp is during the first read() call by the player for the config.ini file.

So Hijack has not yet finished parsing config.ini, or applying macros etc..
Which should not affect GPSapp (assuming it's not using AC/DC/.HOME/WORK macros etc..).

But.. perhaps this causes Hijack to muck up when somebody else (GPSapp) reads config.ini at the same time..

I'll look into this ASAP.