As i suspected after 3 days of trying. Issue was in old wallet.dat file. It didn't have some hidden new master keys or private keys. The amount of displayed addresses didn't change. But after i used latest wallet.dat all transactions showed and funds was taken out swiftly because now i need new wallet due to, to many manipulations trying to fix it.
Which wallet.dat are you talking about? Wallet files for Electrum? or actual wallet.dat files for Core?

I'm still very confused as to what the actual issue was here... because now you're talking about "hidden" master/private keys?

Can you just answer one thing for me... when you imported your "5 keys"... how many addresses were showing in the Electrum "Addresses" tab?