Are you sure you're using the same date range? If you're using Max, then you're not, as ^FTMC goes back to 12/1/1985 while ^GDAXI only goes back to 11/1/1990. If I enter a custom date range of 11/1/1990 through 10/24/2015, I get:
which, other than the dates it chose to use as labels on the x-axes, look identical.
(I tried to add the URLs of the charts, but it looks like the Yahoo! URLs don't include the comparison symbol, which makes them useless for this answer. They're easy enough to construct though, just add the secondary symbol using the Comparison button and set the date range using the calendar button.)
On your PS, I don't know, as you can see by my charts it even chose different labels when the date ranges were identical (although at least it didn't scale different dates differently), so maybe it's trying to be "smart" and choose dates based on the total amount of data available for the primary symbol, which is different in the two cases.