The problem is that the conversion tools don't offer support for the VB6 Graphics commands or the VB6 printer model. Plus you get into a lot of corner cases when dealing with ActiveX controls. I know our own CAD/CAM applications won't translate over with any conversion tools as a lot of tweaks are built into the UI to make it work smoothly with the VB6 Form Engine.
These are things that conversion tools fail on as the WinForm Engine requires it's own tweaks. The same thing was experienced when our software moved from DOS to VB3. Sometimes there is no substitution for manual conversion.
With that being said, there are somethings you can do to make conversion considerably easy. First make sure your application is built in layers. This way you can convert one layer at a time, test and continue on. It also has the advantage of leaving you with usable software at every step. I recommend starting at the top (form) layer and working your way down.
Make sure anything that is VB6 centric and not Basic Centric is behind an interface. When .NET first came out several years ago I created a Canvas Interface and implemented that using the VB6 graphics command. I use the same Canvas interface in VB.NET except now it uses the Graphics Object. The same was done for printers.
Nearly all the code was moved out of our forms into classes that the forms called. The forms themselves implement an interface that the UI Classes used. When we switched to .NET we have a precise definition of how the form interacted with the rest of the system and form conversion was considerably easier.
All of these steps where done in VB6 and put through our normal release Q&A process. Then afterward we started the conversion.