I've managed to get the notification flicker bug in Windows, but only while the node is catching up (before the DB initializes). It ends as soon as the DB is ready (balances and ledgers are displayed). Is this consistent with what you get?
Maybe. The reason why I say maybe is that when I rebuild&rescan Armory takes many resources (although it is much faster from version to version) and bitcoind is blocked as long as Armory has finished. So when Armory finished, Core gets on verifying last 7 blocks and after it has started its network threads this issue occured. And after I get a stopblockingloop and I try to close Armory properly, ArmoryDB stays opened in the background.
So if my PC would be faster maybe this issue would only occure like you said in the beginning before Armory has started ArmoryDB, because Core might be finished starting it's network threads before Armory starts its DB.
But I've let only Bitcoin Core run over night to catch the up the latest missing blocks. Then I've restarted my PC and executed Armory again. The only flags in bitcoin.conf I'm using are "-server=1; -wallet=***; -walletrbf=1". So now Armory finished building the db (haven't any wallets loaded by now) and after bitcoind verifyed the last blocks it immediately connected to Armory. There hasn't been an exception in the log files and additionally the last 2 missing blocks were pushed over to Armory. So I'll load now my wallets in Armory Offline and start Armory again to let everything scan. The connection label is still purple and indicates that Armory has no RPC connection (just P2P), but maybe that label isn't working properly?
I think this issue occurs when there are many latest blcoks left and Core tries to connect to nodes that use a fast connection (because I've read once depanding on s.o. internet connection, Core selects between 2 modes; speed and legacy I think), so when Core tries to find other nodes that support this mode it gets very busy and Armory throws a stopblockingloop because it cannot run it's threads properly and connect over RPC any more. So when there are only a few blocks left, after I restart Core, it doesn't require so many resources that Armory blocks. At least that's what I'm thinking the issue could be.
I will try now scanning my wallets and report on that if everything has gone well or not. But thank you for your involvment goatpig, I really appreciate it!