T50 firmware update causes loss of custom settings.

T50 firmware update causes loss of custom settings.

I've got about 100 model T50 units running Ubuntu. We are in the process of upgrading them all to version 1.037 via FTP and I'm running into the following concerns...
1) Display settings seem to be nearly always lost. Many of our end-users have two screens, whereby both are set at a non-default resolution. Upon upgrading the firmware from 1.028 the devices go back to Mirror mode at the highest resolution. This is a pain having to figure out what it was before imaging and then having to set it properly afterwards.
2) After imaging is complete, they don't re-download the ini file at first boot. If they do, they're not processing it because they don't auto-login like I have set in there.
3) Do they only look for .ini file configuration at boot time? Is this configurable? I'm hoping to get them to download the firmware upgrade ahead of time so they can just be rebooted once but what seems to be happening is that I have to reboot them once just to get them to get the config change that tells them where the upgrade file is. We have some other models, such as the C00X and they seem to pick up changed configuration files fairly quickly, so they only need one boot to install. The T50 units need 2 restarts--once to get the changed file and another to process it.