Logged In: YES

The problem is not in jakarta-regexp. The library finds ^M
if the line contains it. But we apply it to lines we get
using LineNumberReader which eats all ^M (see
LineNumberReader documentation).
So, in current checkstyle's version the only way to find
^M is to write FileSetCheck for this.
Perhaps we should reconsider algorithm we use to get lines of
files so it will not eat annecessary ^M (if it's possible)