Hi RFSTech,
Thanks for letting us know. The iPhone OS keyboard has been problematic when using levels of screens. In the early days we had to write a "hack" to work around that problem. It had looked like Apple had finally addressed this in their iOS 4.2 update of the developer tools, so we decided that it would be better to use the "official" solution for this. Alas, you are the second person who has written us today about this, so I think we will have to revert back to our old "hack" code (which worked about 99% of the time, but wasn't perfect either).
Just so you know, you do not have to reboot the phone. What you will need to do is "quit" the app. First tap on the home button to exit the app. Now double-tap on the Home button. This will bring up the "running" apps on the very bottom of the screen, where the apps such as the Phone, Mail, Safari and iPod usually are, and the top section of the screen will be grey'd out. Find Time Master on the bottom row. Tap and hold on Time Master. The bottom icons will start to wiggle and will have the little red circle on them. Tap on the little red circle to quit Time Master. It will disappear from the items. Now you can relaunch the app and the keyboard will not be in the way. If you have a lot of apps running, you can also quit some of them to free up memory.