I never use compressor for this. I export "Using Quicktime Conversion" and use the following settings:
Click "Settings":
* Compression Type: H.264
* Frame Rate: 29.97
* Key Frames: Automatic
* Data Rate: Restrict to 8000 kbits/sec (since this is being converted to FLASH, I would give them this clean high data rate)
* Quality: Best quality (Multi-pass)
Click OK. Now click "Size":
* Dimensions: Custom 1280 x 720
* leave the 2 boxes below that unchecked
Click OK. Now check the box "Sound" and click "Settings":
(If the movie is going to be re-compressed, use the following)
* Format: Linear PCM
* Channels: Stereo (L R) unless you have some other mix going
* Rate: 48.00 khz
* Quality: Normal
* Sample Size: 16 bits
Click OK.
Uncheck "Prepare for Internet Streaming"
Click OK.
Choose your path for the file to export to - click "Save"
When life gives you dilemmas...make dilemmanade.