[Palsa-San]

Originally Posted by Dark Wing

From what I understand there was a dispute between the anime producers and publishers of the manga. The anime Overtook the Manga and went to its own conclusion in season 2 while the manga went on hiatus for months until it was finally Cut Short with a Deus ex Machina (and an apology for doing so).

A new manga series is currently being published under the name Rozen Maiden Tale. It's an alternate universe story starring a much older Jun Sakurada, which follows what would have happened if Jun had responded "do not wind" to the initial letter, and crosses over with the original universe.

Spoiler for A few chapters later in the manga:

After a few chapters, the story then shifts back to the original Jun via a bridge-arc and the plot resumes where the original Manga ended, making Tales, despite what it initially looked like, an actual continuation instead of an Alternate Universe spin-off.

The reason for the second manga was do to a screw-up on the magazine company's part, as a result, Peach-Pit had to do a fast rewrite of the 7th volume, which was significantly smaller then the previous volumes.
Needless to say, they left the magazine company shortly after that.
Also:

Spoiler for Spoiler about the recent chapters:

Though the series' focus returns to the regular Jun, in the most recent chapter the other world's Jun is brought back into the story.

I haven't heard anything about a dispute between Peach-Pit and the anime producers, but since Peach-Pit has taken the series in a different direction then they had originally intended to go, and the anime producers altered quite a bit themselfs with Träumend, its not too surprising why they would make changes to it.
Then again, there is no telling what Peach-Pit and the producers of Träumend talked about prior to releasing it; though it may seem unlikely, it is possible that they may have had Peach-Pit's approval on the changes in Träumend, on the grounds that if the anime is too similar to the manga, a lot of people will say: 'I've already seen it', and not bother with reading the original.