Updated iPod now slow synching to iTunes???

I just got back from 18 months travelling, during which time my PC (with iTunes) was continually switched off, and my iPod was travelling with me. Upon returning I had a few weeks back on my PC before I reconnected the internet at home, during which time I had my iPod connected via USB to my PC and everything continued to work as it had before I left, apart from when I clicked into the iPod "drive" on my HD I got a threat warning for a file "I-Worm/BrontokX Data Graffiti.exe". I have never heard of this worm and so far detected no weird behaviour in either the iPod on its own, or iTunes, or accessing the iPod through iTunes (synching etc). I didn't want it to automatically quarrantine any files on the iPod itself, so I did nothing. At this stage the versions of both iPod software and iTunes were those from February 2009.
I recently reconnected the internet and firstly restored the iPod to factory settings just to be safe with respect to the virus threat warning. I then updated both iPod software and iTunes to current versions (iTunes version 10.0.1.22). I then re-synched my iPod.
The first thing I noticed is that things are MUCH slower now. Whereas I used to be able to synch new contact at the rate of one new song every second or 2, synching my library from scratch again took a VERY long time, up to 1 minute per song, or about 8 hours for 15GB of media.
Secondly, I keep my media on an external hard drive (due to space on my PC) and I find that I'm having relatively frequent issues now with iTunes "losing" my media and not being able to find it on the external drive (little "!" appears next to song etc), and not being able to find the connected iPod, which never happened on the old versions before I did the updates. Closing and restarting iTunes does not fix it, but restarting the PC does.
Thirdly, now that I have re-synched, the media now seems to be taking much less space on my iPod. Before the update, I had virtually filled my 16GB iPod nano with my entire library. Now, the same library takes barely more than 12GB of space on the iPod.
I guess my questions/issues are:
* Any ideas about the "virus" threat "I-Worm/BrontokX Data Graffiti.exe"? I assume that restoring the iPod to factory settings would have removed any issue but should I be more worried?
* The new versions of iTunes/iPod software just seem to be more, well, jittery than what I had, even if it was versions from Feb09 ("losing" my media, "losing" the iPod, taking far longer to synch etc)?
* Why would media that took 15GB of space on my iPod before the software update, now take only 12GB? I'm worried that stuff is going missing but I can't go through 3,500 songs individually
Any ideas/hints/tips/comments welcome

1st Gen minis required a connection to the power adapter to complete the Firmware update. AC adapters were provided in the box with all 1st Gen minis. 2nd Gen minis do not need this step.
You'll need to find an adapter to complete the process. Sometimes an auto DC charger can also work.
No way around this requirement for the 1st Gen mini (and some earlier iPods as well).

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