What does the "Navigation timed out but sync point met." message indicate when an FTR script is run?
The "Navigation timed out but sync point met." message indicates that IE is telling the script that a specific component on the page did not completely download. The script ignores this component for timing purposes if the sync point (the click needed for the next instruction) is available. The scripts job is to load the whole page, time it, then move on. Once the script has decided to give up on a component, it flags it as didn't complete, it does not include it in the timings, and moves on.
In FTR 4.5.x you can not suppress the "Navigation timed out" messages in the recorder, but they will not affect playback or timings on the player. In FTR 5.x you are able to suppress the error by switching it to an info severity level in the FTR error overrides option.