When posting a certain resolution in a RU ticket ( -r4 for example) RU detects
this a revision 4. Can we prevent auto-linking if there is a hyphen before the r ?

Test: -r2 ar2 r3

Another test in r12312

Fixed by looking for " r[0-9]+" instead of "r[0-9]+"

r1234  This doesn't work when the revision is at the beginning of the sentence.
Is this fixable?

Not trivially, at least it's not something I know how to do... :)

If roundup uses the python re module you can use \s to match all white space 
characters.
http://docs.python.org/library/re.html

Nothing isn't a whitespace character.

A newline should match the beginning of input. You didn't even try it did you?