Only the SEs will be able to tell you :)
There were legions of discussions on this very subject when it first occurred. Some got removed from some forums as there were potential legal issues with application providers (as some were named). Some got quite heated and speculations were on IP reverse look-ups, some on toolbars, some on if there was identifying code on websites (if you were a reseller or affiliate, perhaps), some people just denying it could have happened (until they were in some cases sent a copy of the SE e-mails, not only confirming the ban and the cause - but also citing the applications being used - even then, some accused the senders of sending faked emails) and a load of other suppositions.
Lots of theories but no conclusions, unfortunately.
But at the time, it was speculated that ranking reports could be run on competitor search terms and maybe could get them banned. Never happened that I am aware of, though.
But Google does specifically state that you should not use such tools - even naming one specific application:
If you want to break their rules, then fine. As stated previously, it may work perfectly OK for you.
It may also be worth looking at this old thread: [webmasterworld.com...]
Particularly the comment made the then "GoogleGuy"!
To summarise he says that if you don't want to believe that they can identify queries from automated rank checkers "..you are welcome to believe that..".