You CAN set pathnodes to be ignored by vehicles, and also to be used exclusively by vehicles. One reason behind them standing around at the base sometimes means they don't have a proper path to the flag and back. They also might be just "sitting in vehicles" because there isn't a full path to the flag with all white paths, also might not be a vehicle exit node assigned in the flag object to tell the bots when it's supposed to get out. The blue problem might just be them taking the absolutely shortest route to the flag.
Reading this is alot better to understanding navigation than simply looking at other maps too.
It would help ALOT if you didn't have the map as one giant static mesh, just throwing that out there.
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