BIG BUMP (9 years later)...
We're having this same problem (rotated fills after exporting). I didn't experience this at my previous firm, so I assumed it was a translator setting. After fussing with this for the past 2 days, I think it's a bug.
Under Methods, we have
Export all Fills "as is" selected and none of the boxes checked. In the resultant file,
ALL Fills are Distorted
and oriented in the same direction. Any linear Fills have to be checked and manually corrected as needed (big pain).
MacBook Pro Apple M2 Max, 96 GB of RAM
AC27 US (5003) on Mac OS Ventura 13.6.2
Started on AC4.0 in 91/92/93; full-time user since AC8.1 in 2004