Yes, some discomfort may occur during the initial learning stage until you get a bit more used to it. I can assure you that in the end you'll find Colemak to be much more comfortable. Since you say that it also happened to you while learning Dvorak, I'm pretty sure that it's not a problem with the keyboard layout, but maybe linked to making more errors, or not using a correct touch typing technique.
Here are a few tips:
* Use the Caps Lock key to correct errors using instead of the Backspace key. You should also do it on your work computer if you can using the Registry remapping to remap Caps lock to Backspace.
* If you find it practical to switch your work computer to Colemak as well, even better. You'll make less errors if you stick to one keyboard layout.
* Focus on accuracy instead of speed. Type slower with less errors.
* Make sure you're hitting the right keys with the correct fingers, as indicated on the chart of the Learn page.
* Moreover, make sure that you're not correcting errors with the wrong finger/hand. e.g. if you try to hit the G ('T' on QWERTY), but instead you hit J ('Y' on QWERTY) by mistake with your right hand, you should never try to correct the error by moving your right hand finger from J ('Y' on QWERTY) to G ('T' on QWERTY), but instead type it with your left hand. That movement could strain your hand.
* Discomfort in the right hand can sometimes occur due to the thumb. Try pressing the space bar with your left hand instead, and see if that helps.
* Right hand discomfort can also be caused by the mouse. You might finding yourself to be using your mouse more often because you're not completely comfortable using the keyboard. Try to use keyboard shortcuts instead of using the mouse.
* Take typing breaks more often.
Edit: I've found out from your blog that you decided not to remap Caps Lock to Backspace, which explains why felt discomfort in your right arm while learning both Colemak and Dvorak. The Backspace alone add 15%-20% of finger movement. Using Caps Lock instead of Backspace also helps to balance the load between the hands. Error rate is very high when learning a new layout, and extensive use of the Backspace key could explain the discomfort you were experiencing.
