Any significant keyboard change will require some adaptation time.
For example, I went from a traditional keyboard to a Kinesis Maxim, which was a traditional layout but split. That required a bit of typing adjustment, like what you mention.
Then I switched to a Kinesis Classic (old version of the Advantage, PS/2 port). Now that was a pain, literally. Having to interrupt decade-old touch-typing muscle memory was annoying, and I actually experienced slightly increased pain (tendinitis) for the first several days.
Within two weeks, though, I was automatically using the new arrow key position and thumb keys (Ctrl, Alt, Home, End, PgUp, PgDn, Backspace, Delete, Enter, and Space) smoothly.
My change from QWERTY to Dvorak was even more troublesome and a bit painful. I would say it honestly took me about two weeks to become even barely functional, and a year to become completely proficient. I'm skeptical that I've ever hit the same WPM that I had on QWERTY, which I mastered while still an adolescent. Not that it matters, I just think a bit more and type a bit less now. :-)
Edit: for the record, I absolutely DO NOT advise learning Dvorak. Its ergonomic benefits pale compared to the mechanical keys, split wells, etc. Also, it means lots of key remapping for games, copy/paste shortcuts become kind of arbitrary, and so on. Stick with QWERTY, but use better keyboard hardware. Learn Colemak if you absolutely insist on the 1337-ness of 'superior' layouts.