Based on your description here and the link you provided, it seems the rotation or flipping you find may be an issue with FSL's GUI and FLIRT alignment program. You may need to reorient the data to another orientation (LPI?), but you should probably ask on the FSL list server instead.

You could use one of the alignment tools in AFNI like align_epi_anat.py to do this instead. That script only works with AFNI format datasets, so you would have to copy the data to AFNI format first. Note you would not align the tractography volume from TrackVis directly but instead apply the transformation from a full brain volume like a B0 or FA volume alignment to the AC-PC anatomical dataset. See this previous post for some ideas on this:

[afni.nimh.nih.gov]
<[afni.nimh.nih.gov];