Sorry to hear about the lag problems you have been experiencing. As you know tracking down the cause can be a tough job.. however we will do our best to help.
1 If I understand you correctly you have just formatted your drives and reinstalled Windows and your applications...Is that correct?
2 If "yes" then its not likely to be malware related, unless you became re-infected almost immediately.
3 Have you tried booting into safe mode with networking
and checking to see if the lags persist?
Please be careful when operating in safe mode with networking as your protections (anti virus etc.) will not be providing you with full or often any protection.
4 Check task manager in normal mode
and see what is using your CPU cycles during the period of lag..... you will need to monitor the task manager
for some time continuously to see if a scheduled event or a service of some kind is being triggered and causing the lag. (A program "calling home" to update itself, Windows update, your AV updating or checking in or a whole host of stuff that regularly utilises you computer system resources could be responsible.
5 Try setting up a new user account (via control Panel) log on to this account from a cold boot and check to see if the lag still happens.
6 Power cycle your modem/router and then reboot your computer...any better?
7 Are you using a proxy server? or any P2P file sharing application? (torrents etc)
8 If you are using a wireless connection have you checked for interference from other electronics working on the same or similar frequencies? (baby alarms, DECT phones, Microwave devices etc?
9 Have you tried releasing and then renewing your lease via ipconfig? and then flushing your DNS resolver cache?
10 If using a WAP/router/modem please try a different channel to avoid any potential conflict with a neighbours router set up.
10A If using a wireless connection, try using a wired connection (ethernet cable) and do a further test to see if lag persists.
11 From a command prompt please run the following command when the Internet is not lagging, and copy and paste the output into your reply, followed by a repeat of the command when the computer is lagging (you will need to make sure your timing is good and please run the command at the beginning of the lag (within a second or so!)
Please use copy and paste (everything in blue) to ensure that the syntax is maintained:
cmd /c "ipconfig /all> postme.txt & ping bbc.co.uk >> postme.txt & notepadpostme.txt & del postme.txt"
(Press the enter key to execute the command).
11 A broad brush approach is to try and determine if a Windows problem exists or if the cause is elsewhere (like in the modem/ router, house wiring etc.,...so firstly using an Ethernet cable connection (not using wireless) download a copy of Linux Puppy available from here:
12 burn the iso (100Mb or so in size) to a CD as an image, (it must be an image, a plain copy will not work) so to make it easy use ImgBurn available here.
13 Via the BIOS set your computer to boot from CD/DVD as priority one and with the Puppy CD in the tray save the changes in your BIOS and exit and your computer will boot into Linux Puppy, follow onscreen directions as to language keyboard etc.
14 Allow/get Puppy to set up the drivers for your wired (ethernet connection) and then connect to the Internet you may ned to download a browser... and carry out your test for lag again....
If the lag persists in Puppy then we have to look to your router house wiring modem or ISP for the likely cause... however if the lad is not apparent in Puppy but is in Windows then we will know where to focus our attention.
If you post back with your findings step by step 1 through 14 then it will help us suggest the next steps for your to take