Fixing warnings.

Refs #1777.
Fixing overloaded virtual warning.

@friedmud, I think the threadJoin() function prototype was wrong,
it took a UserObject reference before... this was also part of the
warning and is addressed by the patch.

Refs #1777.
Revert "Merge pull request #3147 from aeslaughter/auxbcs-3021"

This reverts commit aaa219b7fa6370a0bdc58a74b6f76ab22d312f3d, reversing
changes made to 5613ebb783ccf5c1550ea1ba3321c0336f49f013.
Merge pull request #3164 from jwpeterson/warnings

Fixing warnings.