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It doesn't matter if I shut down properly or not, every time I start it up it gives me that "Improper shutdown detected" nonsense and tries to scan the disc...a process which looks likely to take days if I ever allowed it to complete, which I haven't.
Second problem: every startup automatically calls up the SYSTEM folder.

Dr. Mysterio, maybe you have an error that needs fixing. Mine did that quite often and finished the process in seconds. Perhaps you need to set it to fix errors, turn off any screensaver and just let it do it's thing (overnight?). When it's done - defrag (may also take a WHILE).
HTH.
Ed in Texas.

Start ScanDisk. Set Standard mode, run Scandisk.
Start ScanDisk. Set Thorough mode, run Scandisk and let it fix all of the built up disk drive errors. Take a long break while it runs to completion.
Start ScanDisk. Set Standard mode, run ScanDisk in standard mode again and last. Reboot.

Dr. Mysterio,
Have you done/been to the wind_ws update site?
Sounds possibly, like this, might be of some help.
Second problem; Could be called from the start menu, startup folder. Could be called from the win.ini, could be a program calling for a file....ect. When did this start happening?
Have you updated your drivers, for your motherboard, video, sound, modem, ect.
Have you visited the wind_ws update site, recently?

I would've done the full scandisk and defrag earlier, but I've done those before with no effective result. However, I did them over the past day - thorough scandisk found no errors, but standard scandisk had two instances where it seemed to find something wrong and advised me to run thorough. (I ran standard first, then thorough)
I then ran defrag...last time I did that I had to do it in safe mode, but it worked normally this time.
Then I restarted the computer and the false "improper shutdown" isn't a problem anymore; doesn't do the automatic scandisk now. So, thanks!
edit - oh crap, sorry JackG - I didn't run the standard again before restarting. I'm going to do that now.
However, the SYSTEM folder still comes up after startup. I have visited the windows update site and updated accordingly some time ago, BUT...I have since had to re-install windows. Both of the problems I've complained about in this thread were in effect before the re-install, and before that update. (in fact, I didn't like that update at all...didn't like what it did that IE) I have not updated any drivers or made any hardware tinkerings since I first got the computer.
This has been happening for some time; it's merely an annoyance that hasn't really affected anything, or I would have addressed it earlier.

Dr. Mysterio,
"Both of the problems I've complained about in this thread were in effect before the re-install, and before that update. (in fact, I didn't like that update at all...didn't like what it did that IE)"
The specific update I linked, has nothing to do with "IE" {Internet Explorer} It's detailed, in the link.
Did you check your statup folder, in your start menu? Did you check in your win.ini, under [windows]? {start, run, type; win.ini Press Enter}
Or you could use the system configuration utility {msconfig}. Look in the Startup (Tab), for any reference to just the system folder. Look in the Win.ini (Tab),
[+][windows]Might even try the "Cleanup" (button), on the Statup (Tab).
There are more, but, start there. When it opens at startup, is/are any file(s) highlighted?
To close, you should keep your drivers updated. Just an opinion.
CrazyOne

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