The Exelixis insertion f03691 is annotated in FlyBase (and by Exelixis) as mapping to the CG7077 gene on 3R.  While curating alignments to Release 5, I noticed that the flanking sequence is a chimera with segment 1-54 aligning to a site on the X and segment 46-344 aligning to the site on 3R.  I obtained a stock with this insertion from the Bloomington Stock Center (#18683).  When I crossed f03691 males X w1118; TM3/TM2 females, all of the female progeny are w+ and all of the male progeny are w-.  Therefore, it is likely that the segment mapping to the X chromosome is the true flanking sequence.  This segment maps the insertion site at  X:12647341 (+) (Release 5).
A second similar case is e00899 (FBti0041444).  This is currently annotated in FlyBase as an insertion on 3L in the CG6938 gene.  I noticed that the flank determined by Exelixis has two segments: the segment adjacent to the end of the vector maps to 2R and the vector-distal segment maps to the 3L site in CG6938.  I obtained a stock from Bloomington and found that the w+ transgene marker segregates from chromosome 2.  Assuming that the flanking sequence segment mapping to 2R is correct, the release 5 coordinate is 2R: 12708189 (+).  According to release 5.2, this puts the insertion in 53D11 between CG5550 and CG34459.