Has anyone else had audio sync issues with their nanoFlash files and Premiere Pro CS5 (5.0.3 - last update)?

I recorded input #1 into both channels on my EX3 and the first clip is out of sync by 2 frames with the 2nd channel being delayed by 2 frames. Then, the 2nd file goes out of sync part way through which is shown in the attached image.

This is a major PITA to fix. I have had this issue once or twice before but nothing like this with over 2.5 hours of video from a single event.

Dear Steve,

I will ask our lab manager to look into this.

Please provide us with the details, so he can attempt to duplicate this issue:

Camera
Embedded Audio or Analog Audio
MOV, MXF, or MPG
Firmware version, I assume 1.6.248
Codec (Long-GOP or I-Frame Only)
Bit-Rate
Frame Rate of video
Whether cranking or 3:2 pulldown or if any other special features were in use.

1) Camera: EX3
2) Embedded Audio or Analog Audio= Embedded via HD-SDI
3) MOV, MXF, or MPG= MXF
4) Firmware version= 1.5.126
5) Codec= Long-GOP
6) Bit-Rate= 50Mb
7) Frame Rate of video= 29.97p
8) Whether cranking or 3:2 pulldown or if any other special features were in use= none. I had E to E Direct and Record PSF>Prog enabled. Max File Size was set to 100%.

I didn't update the firmware because I wanted to use the current firmware because it had been reliable in the past and I had no SxS backup for this event and the following night's event.

Dear Steve,

Your nanoFlash firmware version, 1.5.126 was from June 2010.

Since then we have made changes in the audio sync.

However, we will still investigate this issue as I do not understand why the audio would be in sync at the start of a single file and then out of sync later.