you DID extract the reference fies from the archive? and then did try to open the entity files where you extracted them to ( and NOT the entity files in the program files area)?
but if you just want to DOUBLE the size of your fleet, here is a quick mod of mine for this exact reason
(http://dl.dropbox.com/u/8023186/sins%20mods/double%20fleet.zip), and it is to be extracted into the expansion & version's MODS folder
and my standard advice regarding placement of mods
assuming you have sins 1.193/entrenchment 1.053/diplomacy 1.34(the current non-beta versions), AND your windows is installed on the 'C:' drive, the Mods NEED to be placed here for xp
C:\Documents and Settings\'user name'\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Mods-v1.193
C:\Documents and Settings\'user name'\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Mods-Entrenchment v1.053
C:\Documents and Settings\'user name'\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Mods-Diplomacy v1.34
or here for vista/windows 7
C:\Users\'user name'\AppData\Local\Ironclad Games\Sins of a Solar Empire\Mods-v1.193
C:\Users\'user name'\AppData\Local\Ironclad Games\Sins of a Solar Empire\Mods-Entrenchment v1.053
C:\Users\'user name'\AppData\Local\Ironclad Games\Sins of a Solar Empire\Mods-Diplomacy v1.34
NOTE the first two folders after the 'user name' are hidden , so to see them you must first click on 'tools' then 'folder options', then 'view', then click on 'show hidden files& folders' then click ok, then you will be able to browse your want to the folder. I suggest when you find the folder that you create a shortcut to it on the desktop
NOTE 2 the 'user name' in the above paths is your WINDOWS login user name, eg Administrator
and if the mod you want to use is from an EARLIER sins/entrenchment version place the mod in the mods folder FOR THAT version eg mods-entrenchment v1.03, then download and run my mods updater from the latest version archive which will have the same number as the vanilla sins version number, and AFTER updating the mod(s) to the current version for any mods of pre 1.04 entrenchment ALSO run the manifest maker on ENTITY manifests on EACH of the mods EXCEPT for total conversion mods
harpo