I believe the phone system accesses the same database as the online system - hence the results are the same. The BCIS customer reps also access the same system and have absolutely no additional information to give.
I think the processing is still being done on paper only (as in the dark ages of the INS) and then someone manually goes in and updates the query system. Often, that "someone" conveniently forgets - after all, its not really adding to his/her productivity.
The problem gets worse than that - in the case of Visa renewal and most phases of the GC including I140, the BCIS refuses to let you (the beneficiary) know what is going on with your case (other than the online status. My Visa renewal had been pending for more than 10 months. An RFE was replied to in June and yet there was no news. So I initiated an inquiry after calling BCIS and talking to a rep. After weeks of waiting I get a letter in the mail only to tell me that as per privacy laws, the exact status of what's going on with the application cannot be revealed to me. Apparently, the application belongs to the employer and I have no right to know!
So not only are we stuck with an incorrect online query system, but we also cannot inquire directly with the BCIS on our case status.
I've heard of some people on here contacting local senators who have then followed things up with the BCIS. I guess the time elapsed must be way more than the 360 days (for I140) already indicated on the receipt by BCIS as the processing time required, before the Senator's office will consent to take it up directly.