Partitioning problem with windows vs. linux

[Michael Wiktowy]

Greetings all,
I have an odd problem happening that I have experienced on a Fedora Core
install in the past and in recent history also.

Background:
When I try to set up a dual-boot w2k+linux system (resizing w2k
partition and filesystem, verifying w2k is happy after resize,
installing FC), w2k is not happy sometimes on some systems. It will
start to boot, switch to its more graphical starting windows boot
screen, get halfway though and then blue screen [1] with a
BOOT_INACCESSABLE error advising me to do a chkdsk /f and giving me no
means of doing so. The recovery console on the install media doesn't
seem to do the trick on this system (Dell GX280 with a SATA drive)
either. [2]

Specifics:
I have narrowed down the problem to w2k not liking me simply adding
extra partitions to the disk.[3] I boot to Knoppix and use fdisk to add
some partitions (to try avoid the "anaconda changing the CHS values in
the partition table with a buggy bios" issue) but as soon as I do, w2k
becomes unhappy. I can subsequently remove the partitions and w2k is
content again and boots normally.[4]

Am I doing something wrong by using fdisk /dev/sda to add some primary
partitions after the w2k one?
Does Partiton Magic do some other magic that makes w2k happy?
Is there a way to make w2k insensitive to partition table edits that
don't affect its partition?

I have set up systems to dual-boot w2k/xp+linux on a single disk using
grub as the boot loader before. I am a little baffled why some systems
cant seem to handle this. Are there some BIOS issues at play here.

I have a "dd if=/dev/sda bs=512 count=1" of both the mbr that works and
the one that doesn't if anyone has the expertise to dig into it and
figure out if this is a bug with fdisk and certain systems or just w2k
being stupid.

I know the work-arounds for this type of weirdness (use a separate disk
for linux, use the ntloader instead of grub) but I am interested in
tracking down and helping solve this issue rather than avoiding it.

Thanks in advance for any insight/guidance you can provide.

/Mike

[1] I think this is the time when w2k does some sanity checks on the
drive as this is also the time when it will start a chkdsk if one is
scheduled.
[2] I don't think that the recovery utilities on the w2k install CD in
rescue mode understands SATA at all. Maybe making a rescue floppy after
w2k installation might help but I have not tried that.
[3] I have made dd images of my w2k partition and mbr in a working state
and have played around extensively to try to narrow down the problem.
[4] This seems to indicate that there is no permanent overwriting of
anything that occurs when I add the partitions ... make the problem that
much more baffling.