You could have run 8.0.8 and still use GP 4.1, it's not necessary to run 8.1 for GP 4.1, it's backwards compatible up to PAN-OS 7.1 I don't think it's recommended yet to run 8.1 in production, new releases always tend to have a few issues. The same goes for GP 4.1... it looks nice, and I'm sure it will be a great client, but it's not just there yet... wait until GP 4.1.2... I would downgrade the firewall to 8.0.8, and use GP client 4.0.7 for now, despite the interface looks dated, it does not have the problems you describe and it's very stable.
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