Bug: Bitrate changes on export from Premiere Pro or After Effects
 

From the Adobe blogs:

There is a known bug when exporting from Premiere Pro or After Effects involving modified bitrate values. If you modify the bitrate value of an encoding preset, the default bitrate for that preset will replace the custom bitrate you specified.

As a workaround, you can:

Manually change the bit rate of the video file you are exporting to the desired value once the file is in the Adobe Media Encoder encoding queue...

-or-

Add your video to the list of files to encode from Adobe Media Encoder itself. You can drag a file into the list, or click the Add button and select a file on your computer.

Note: To add Adobe Premiere Pro sequences or Adobe After Effects compositions to the list of files to encode, you must use the File > Add Adobe Premiere Pro sequences or File > Add Adobe After Effects Compositions menu commands. These file types cannot be dragged into the list of files to encode.

What version(s)? The way you wrote it, it sounds like CS4, because you mention the AME queue.

Can you please confirm?

Yes, is CS4.

When I am encoding using AME with the rapiHD preset in CS4, the bitrate on an hour long encode in Blu-ray dropped from the 25 range down to 6 with obvious pixelation and breakup several times for several minutes of footage each time.

Is that the same bug?

I'm not familar with the rapiHD presets. It's my understanding that if you change the bit rate of a preset, that change does not make it to the Adobe Media Encoder. After queueing the item in AME, you would need to edit the settings to update the bitrate.