So I guess the gap-limit means its show many addresses to check balance on after the last address with a balance, correct?
Close... more correctly it is X number of
"unused" addresses, before it stops looking for coins. This means that an address that might be empty now but did at some time contain coins would still be counted, so the gap limit count would be reset and Electrum would continue searching.
So, the "danger" here with the "red" addresses... is that should you choose or need to restore your wallet for any reason, it will not automatically find the addresses in red... until you have used addresses in the gap which forces Electrum to then look X more addresses along the derivation path.
What is confusing is that it seems to occasionally marking them as red and sometimes not? is that correct? If so, it would seem that you must be hitting a malfunctioning server that is lagging... and not detecting a transaction in an earlier address, so it makes it seem like those addresses are beyond the gap limit... when in fact, due to this "missing" transaction, they are within the gap limit.