EDIT: OK so it looks like Cydia is giving up the ghost and having some major issues. I've re-uploaded 4.30.05 for those of you that want to save 4.3.1 via APPLE. Hurry up and do so before 4.3.1 is no longer signed.
To save your SHSH via APPLE instead of CYDIA (the default) go into Advanced options and UNCHECK the box that clearly says: "Request SHSH From Cydia" then click 'Apply Changes' then select your device then click 'Save SHSH'
Also, If you want to save 4.3.2/4.2.7 get the updated 4.32.01 as there was a file missing in 4.32.00 XD.