I had similar problems.

Excerpts from internet.computing.netbsd.port-mac68k: 31-Oct-96 system
clock time by jbyler@MIT.EDU 
> Here's my situation.  The clock is set correctly in MacOS.  My
> location is also set correctly in the MacOS Map control panel.  And I
> have put a link to the correct time zone in /etc/localtime.  Given
> this situation, the unix system clock (output of 'date'; timestamps on
> files) is several hours off.  If I point /etc/localtime at
> /usr/share/zoneinfo/UTC or .../GMT then 'date' gives the correct time,
> but marks it as GMT, not EDT.  I suppose I could just leave
> /etc/localtime pointing at UTC, but that seems like a kludge solution.
> I have heard that there is a compile-time kernel variable related to
> all this, but I have also heard that this variable is obsolete.  And
> in fact, it doesn't appear in the kernel configuration files.

If you can get the correct file symbolically linked to /etc/localtime/
so that EST (or whatever) show up correctly in the output of date, your
halfway there.

I then added the following command to root's crontab:

0       */2     *       *       *       /usr/sbin/rdate <ts>
>/etc/date.corrected

Replace <ts> with the name of a machine on your net which accepts
daytime queries.

That'll keep the clock set correctly, and I think should take care of
any drift.

Hope this helps.

-c
 _____________________________________________________________________
|Chris Mason - cmason@nyx.net  cmason@cmu.edu  http://ros.res.cmu.edu |
|"You can always count on a murderer for a fancy prose style."-Nabokov|
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