Still digging into this issue, but I've already reproduced this problem on OSX on eclipse versions prior to Juno (4.2), with the Java and PHP packages.
I do not see this issue on Juno, Kepler, and Luna on OSX - which are all 4.x eclipse version lines, while Helios and Indigo are 3.x.
With the info I have so far, it appears to be a difference in the signature format between eclipse versions, most likely exposed by a change in the build process some months ago.
FYI, I have not tested yet on other operating systems, and probably won't for at least a few more days, since I'm on vacation.
Note, the PHP plugin and several other scripting language plugins on the newer eclipse releases also have another separate issue - they have a dependency conflict with the BrightScript plugin ( a DLTK plugin version conflict ).
So, I recommend installing second, a more up-to-date, eclipse instance (use either the "standard" version or the plain java version - not PHP) and installing the BrightScript plugin there.
Be advised that Luna has not been tested beyond the basics yet, so Kepler is your safest bet at present.