A bunch of stuff. First of all the merger between east and west german railways happened in 1994 that was due to a lot or rail connections having to be rebuilt and a number of high speed lines were built or improved to Berlin. That however cost a lot. Then the German government was thinking about privatizing the railways. To do that a stock company was formed with the goal of turning a profit. So they stopped maintaining tracks and avoided new investment as much as possible for quite some time. In the meantime both passenger and freight railway demand in Germany increased a lot, while very little to no new track was opened. Also the ICE service was increased and unlike most everywhere else, it is run for the most part on improved old track and not new lines. Regional rail and freight run at roughly the same speed, if you consider the regular stops of regional rail. HSR runs faster, so other trains are either in the way or they have to move to the site.
As a result most of the German mainlines are at capacity or above it. As in there is demand for more trains, but the tracks do not have the capacity for it. So if anything goes wrong on any train, it results in a traffic jam, which causes delays for everybody else on those sections. However since long distance trains go through the entire country, nearly all of them do have to cross those sections.
The obvious solution is to built more railway and especially add high speed rail lines in parallel to the current lines. However NIMBYism is strong in Germany and when combined with a strong car lobby, it makes building new lines nearly impossible. Every single project ends up in a decades long planing stage, with mulitple law suits and even with construction you end up with stops, due to legal problems. For the most part the construction work is doing just fine, it is really just politicans being corrupt.
