We recently had some trouble estimating insert sizes with our Mate Pair (aka Jumping, larger insert sizes) Libraries. All the libraries sequenced by Biodiversity and the Genome Sciences Centre (GSC) were shockingly bad, but the libraries sequenced by INRA were very good. For example, according to the pipeline, the GSC 10kbp insert size library had an average 236bp insert size, but the INRA 20kb library an average insert size of 20630bp.
See the histogram for the 10kbp library: