New player here, attracted by Diaspora and since purchased FS2 from GoG. Excellent work, really well done.
Posting here to confirm - TrackIR worked for me fine with Diaspora R1, updated to R1.1 and started getting this reticle issue. Same occurs in FS2, with the January 2014 build (I have the FSO scptrackir.dll file in root). Afraid I don't have any earlier builds, but if it's any help for narrowing it down, whatever changed in the Diaspora versions seem to have triggered it (my FS2 retail and Diaspora installations are on separate drives).
To explain it more clearly, the aiming reticle is perfectly centred on screen regardless of orientation of camera. Rest of the HUD remains in place - makes aiming almost impossible.