We are at ArcGIS 10, SP4 and this issue is still not fixed. Symbols from certain layers fall outside the data frame when exporting to PDF, either using ArcMap or PDFfill. Anno behaves correctly. It also does this when printing or exporting to JPG. All data is in ArcSDE at 10.
We have tried changing layer order, removing layers, recreating the MXD, using the data-driven pages clip option in Data Frame properties and all other sorts of options and nothing we did or things suggested above works. The misbehaving layer jumps to other layers when some layers were removed as a test, so it's not the data layer itself causing the issue.
We finally uninstalled the "upgrade" and reverted to 10 SP1, that works OK. ArcMap 10 SP 2, 3, and 4 all have this issue.
Ray Montgomery, GISP
Sandy City, Utah