The clock in my A4000T has a similar problem, except it GAINS about 9 seconds every 15 minutes :-P
In this case I believe it's my PicassoIV changing the VBlank timing signal frequency which the internal clock (not the RTC) is timed from. The RTC has it's own seperate crystal for this.
Since it's online 24/7, I use FACTS to automatically correct the time every 30 minutes.
As for replacing the battery in your computer, I'm in the middle of writing a do-it-yourself guide to this. My work so far is online at:
http://amiga.serveftp.netLook in the battery replacement section.
The fault finding section is scheduled to be written next, should get onto that in the next few days.