Sounds like dropped frames... could be a number of things... are you caprturing to a seperate hard-drive? Do you have all background processes turned-off?... Premiere Elements might take more resources than Magix?... infact a number of folks have reported this issue over the years. Generally capturing with another program like the freeware HDVSplit that uses hardly any resources allows for a good capture. Premeire Elements HDV capture is pretty bad anyway... no preview during capture, no split by timecode whereas HDVSplit allows this. If your Magix captures are fine I would just use those within Premiere Elements... nothing wrong in using more than one program to accomplish your task.
Paul_LS's suggestion to use DDVSplit is echoed by many. Many on the PrPro forum use it and sing its praises for the reasons that Paul stated. With DV material, many also use SceneAlyzer Live, in lieu of Premiere's Capture module, especially for its better "scene-detect."
All of the programs are just tools in the toolbox of one's workflow. It's like reaching into the toolchest for an flexible socket with a woblble connection, instead of an adjustable spanner, when the need arises. Both flavors of Premiere have pretty good Capture modules, but they are like that adjustable spanner - one size fits all. Often there are specialty programs, that just do a better job.
It's similar with Burning DVD's and BD's, where many author in one program, and then Burn in another, like ImgBurn. For them, it's just the best tool for the job.
All-in-ones can be convenient, but certain aspects of the total workflow can be enhanced by the use of another program at a certain stage in the Project.