could you describe what the windows looks like? i suspect they may be messenger windows. (gray box with an 'OK' button at the bottom most of the time)
edit: im off work, so if it is similiar to the problem i am describing, follow these steps...
- 'start', 'run...' and type: "services.msc" and click the 'ok' button or enter
- go down in the list to 'messenger', right+click and click 'properties'
- underneath 'startup type', choose 'disabled' and underneath 'service status' choose 'stop' and click 'ok'