The idea of JAR should mean there is no difference whether you have a Spainish (for example) or UK issued licence. However, while the qualifications remain the same having had a CPL/IR issued in any state, the simple fact remains, that some NAA's are easier to deal with-with regards to admin and efficiency.
I've heard stories of it taking 3 months to have a type rating added to a non UK JAR licence, and the UK CAA do it as a same day service at no extra cost then a normal service.
(I just paid £600 for a visa for my wife to have it done on the same day instead of 3 months at a cost of £400).
You may pay more at UK CAA etc, but you tend to get a quicker service then most others!
HB