It sounds like the Al is getting oxidized by air exposure.  You might try
back sputtering, if your system allows it (i.e. sputter the substrate a
little instead of the target to clean off the native oxide.)
You might also look into reworking your design so that both metals can be
deposited without breaking vacuum.  Perhaps there is a selective etch (that
will etch Cr but not Al) that would allow you to expose the Al layer

David Nemeth
Senior Engineer
Sophia Wireless, Inc.