RUN/MSCONFIG and in the Advanced area, check the box to NOT run Scandisk at bootup. There are many times when a normal shutdown still gives you this error message at the next bootup....
Something else that could be happening if you have W98SE is that you need the shutdown patch that was made available for that particular OS version only.
You can download it from MS in the W98SE downloads as a separate file or get it here instead...
Win98SE Shutdown Patch Concerns
The patch is designed to correct one of the most common complaints about Win98SE---indeed about Win98 as a whole: Slow shutdowns, or
hangs at shutdown.
You see, Win98 shuts down a PC in a way different from
Win95's method: Win95 shuts down each running component
essentially one at a time, in linear fashion, and waits for
one component to finish shutting down before moving on to
Win98, in contrast, issues a general "shut down now" order
to all running elements, and only waits for those relatively
few apps, services and other components that have to clean
up after themselves of perform sequential functions to shut
down properly. Microsoft's theory was that most Windows
components don't need to be shut down one at a time,
For systems with these kinds of apps and add-ins, Win98's
"fast shutdown" works great: The system responds almost
instantly to a shutdown request and is ready for power-off
in just a couple seconds.
But it turns out that there's a lot more software and
drivers than Microsoft thought that needs the slower, one-at-
a-time shutdown process, and simply don't work well with
Win98's Fast Shutdown. The too-frequent result is that Win98
often is slow or balky in shutting down.
Prior to the release of the Shutdown Patch, the only
workaround for Win98 users was to disable Fast Shutdown--
that is, to tell Win98 to revert to the slower, but more
reliable Win95-style of shutting down. This works in the
majority of cases.
If you're interested in trying that approach, the simplest
thing is to type MSCONFIG.EXE on your Win98 machine's Start
menu's command line. Then, on MSconfig's General tab, click
the Advanced button, and check "disable fast shutdown."
Clearly, this is an inelegant solution, but it does resolve
the majority of Fast Shutdown woes.
Win98SE was supposed to resolve many of the long-standing
issues with Win98, but alas, it seemed to make the fast
shutdown problem worse. So Microsoft created a Fast Shutdown
patch that's supposed to resolve the fast shutdown issues.
If you're running Win98SE, you can grab the patch at
The patch adds new VxDs and DLLs to your system and updates
or adds INF files (all of which address common fast-shutdown
problem areas such as the handling of PCI devices and power-
management software). But here's the kicker: The patch also
gives you a new version of Msconfig. That version is nearly
identical to the old version, except that it does not offer
the "Disable Fast Shutdown" option.
Plus, once the Fast Shutdown patch is installed, there's no
way to uninstall it. So, the patch is a one-way trip--- once
you install it, you're locked in to using it, and the new
versions of the applets , DLLs , etc. it installs.
FYI: These are the files the Patch adds or changes in case
you want to make backups first:
239887UP.inf, Setup Information, 8/17/99, 4:17 PM, 2,623 bytes
qfecheck.exe, Application, 7/27/98, 3:48 PM, 36,864 bytes
Qfecheck.hlp,Help File, 2/9/96, 6:28 PM, 8,042 bytes
3675.cat, Security Catalog, 8/12/99, 1:26 PM, 5,903 bytes
CSETUP.exe, Application, 8/12/98, 9:32 PM ,16,896 bytes
MSConfig.exe Application, 8/11/99, 10:32 AM, 59,392 bytes
tshoot98.chm, Compiled HTML Help file, 7/22/99, 11:12 AM, 240,797 bytes
Pci.vxd, Virtual device driver, 8/11/99, 10:41 AM, 65,919 bytes
apmbatt.SYS, System file, 8/11/99, 10:46 AM, 4,384 bytes
239887UN.inf, Setup Information, 8/17/99, 4:17 PM, 1,632 bytes
configmg.vxd, Virtual device driver, 4/23/99, 10:22 PM, 125,057 bytes
ver_chk.inf, Setup Information, 8/12/99, 12:30 PM, 1,520 bytes
Advpack.dll, Application Extension, 7/15/97, 6:53 AM, 74,960 bytes
W95inf32.dll, Application Extension, 7/15/97, 6:53 AM, 4,608 bytes
W95inf16.dll, Application Extension, 7/15/97, 6:53 AM, 2,272 bytes
If you're using Win98SE and are having shutdown problems,
you might want to try the patch. If you're using a non-SE
version of Win98 and are having problems, try the Msconfig