The problem only exists with footage shot with the flip camera.
That statement, I think, just about sums up the situation. If the initial screenshot you posted is correct, then the Flip films in true progressive mode i.e. 59.94 full frames per second for NTSC. The problem is that VS -- and, I imagine, quite a few other editing programs -- cannot deal properly with that frame rate if you are talking about putting it on a DVD... Depending on what output you have selected, VS will treat such video as interleaved, rather than progressive, and in effect throw away every second frame to make it conform to the international DVD standard of 29.97 fps. That is likely to appear as stuttering, the way you describe it in those parts of your project where you have Flip footage.
VS can produce HD footage which uses true progressive mode, but only in 1280 x 720p frame size. You select it by going to Share > Create Video File > Custom, and then selecting "MPEG Transport Stream Files" as the output format, and adjusting things in the General and Compression tab of Options for that. But I am still not sure that mixing it with DV footage would avoid the problem since if you set VS to produce full progressive 1280 x 720 at 59.94 fps, then in effect it would have to convert the interleaved DV to full frames. That might introduce other problems when viewing.
VS can in fact produce a video which is full 1920 x 1080 in frame size, and at 59.94 fps. To do so, you select Share > Create Video File > Custom, and select AVI as the output format. Then in the Options button, you select one of the AVI codecs on the Compression tab and adjust its properties. On my set-up, this includes DivX/XVid, Microsoft Video 1 and a number of Matrox codecs I have installed for another program.
You can then play such a video back on your computer or arguably even directly on a Blu-Ray player connected to your HDTV, provided the player is rated to detect and play such video on, say, a USB stick drive or external hard drive connected to the player. But you won't be able to burn such files to DVD, Blu-Ray or AVCHD discs since the container format (AVI) does not comply with the international standards for such discs, and conversion of the video will take place, thus reintroducing the problem you have at the moment.
