Controls flipped (mirrored) in certain build environments

Unsure how to reproduce, except with our specific application. Our application uses Flex 3 compatibility mode, and we compile it using the command-line compilers, rather than with Flex Builder. Everything else is pretty standard. The controls are not flipped when we use the 4.0 SDK - it started when we switched to the 4.1 SDK on our build server. Switching back solved the issue. In the first screenshot, we're showing a Canvas via the PopUpManager. The Canvas is mirrored. In the second screenshot, it's just a skinned combo box. The options are mirrored. All components that do not pop up in some way render properly.

Steps to reproduce:
1. Compile Adobe AIR application using Flex 4.1 SDK.

Actual Results:
Certain controls are flipped. It seems like they are on a higher layer. See this post for more information: http://forums.adobe.com/message/3067962#3067962.

Expected Results:
Controls to not be flipped/mirrored.

Workaround (if any):
Revert back to 4.0 SDK.