Depending on which version of Windows you have, there are different ways to control the gain. For VA 9.0.6 (which I use most of the time) the level controls in VA only work in Win XP. In later versions of Windows, you have to go to the Windows sound controller or other installed app (e.g. DTS Audio Control Panel or similar) or both, to control the level from there.
Win 10 and some versions of Win 7 have "audio enhancements", sometimes quite well hidden. Turn them off! Typically they are on by default and cut out low frequencies or echo cancel, which causes analysis problems. It can be a good idea to use a USB mic, because they typically bypass all the hard-to-find Windows sound card controller stuff, as the mic basically has its own sound card in-built. Also, make sure your mic is physically isolated from your computer as vibrations and noise pass easily through shared table tops and mic stands. Some Mac laptops and tablets have inbuilt mics that work well enough (if you can get VA to work on a Mac) but none of the PC laptops I've ever used has worked well using just its inbuilt mic.
If you still have problems, I covered a lot of stuff on collecting data using VA in the video series I did with Robbie O'Brien,
Guitar Analysis and Testing with Trevor Gore, available from Robbie's website.