I guess what you mentioned about FlashDevelop should be FlashBuilder, right?
For FlashBuilder, if you are using RSL model to link TLF. You should change the corresponding settings in the Flex-config.xml. Or You may solve the problem by setting libraries as "merge into code".
For migrate from CS5 to CS5.5, you may check the help of http://help.adobe.com/en_US/flash/cs/using/flash_cs5_help.pdf. In the chapter 9, you should find the detailed steps.
No we are using FlashDevelop, not FlashBuilder.
I figured out the problem. I had to recompile all of our libraries (40+) in CS 5.5. As most of them were still compiled from CS 5, they would have had the TLF Runtime 1.0 still embedded, instead of TLF runtime 2.0.