I'll put on my name nerd hat for you.
The Madelyn spelling was ranked #104 in 2007. It jumped up to 64 in 2008, then jumped a little more, to 59 in 2009. It has fallen a bit, to 76 in 2010 (2011 numbers aren't out yet). Madeline, on the other hand, has held a spot in the 50s to 70s for the past ten years. In 2010 it was at a low of 77. Madelyn and Madeline are next to each other on the popularity list! Madeleine hovers around 300, so it's not nearly as popular as either of the other spellings. If misspellings bother you, that's one to scratch off the list since many people will spell it whatever way is most familiar to them.
As for pronunciation ... this is why I talked about the Madelyn spelling. Madelyn is a style statement. It's updated for the times. There's also Adelyn vs Adeline, along the same lines. People who want the -LYN pronunciation tend to spell it the obvious phonetic way, and reinforce the spelling trend.
Because of the popularity of the -LYN spelling and pronunciation, and its recent growth trend, I assume that anyone spelling it Madeline is doing so because they want me to pronounce it -LINE instead of -LYN. I would guess -LINE for the Madeleine spelling as well, if I met a little Madeleine one day, but I have heard it pronounced Mad-uh-LANE as well.