Strange problems after apt-get upgrade

[reid mumford <reid.mumford@gmail.com>]

I am having some strange problems that I am having trouble diagnosing.  

A week or so ago I upgraded against the unstable release with apt-get
upgrade.  Everything went smoothly but ever since then I've had some
strange problems.
1.  suddenly DMA for my hard drive no longer worked.  I would get an
"operation not permitted" whenever I tried to set the DMA using
hdparm.    I recompiled my kernel and fixed the problem but before the
apt-get upgrade, I know that DMA was working..... How could this
happen?

2. Sometimes when I boot, the login manager will not listen to
anything I type.  I can type (nothing happens when I type) and the
computer freezes for a second or so (according to the second hand on
the clock on the login screen).  I can use the mouse and choose to
login using the command prompt and startx just fine.  This
mad-keyboard disease happens about 30% of the times I boot my
computer.  Not very consistent... strange.

3.  Most annoying of all, I now have a strange glitch where my
computer freezes for a fraction of a second every 2 or 3 seconds.   It
makes it very difficult to use the mouse and makes movies or programs
like glxgears freeze along with the mouse at the rate mentioned above.
 I thought that it was a DMA related problem but after I fixed problem
#1, the stuttering problem still persists.

Does anyone have any ideas on what might be causing the problems? 
These problems were not present before I upgraded and I have tried
booting with ACPI=off and that didn't seem to make any difference.

Thanks for any help...