What did your licence say before you renewed the SEP (Land) - was it "IR-SPA-ME class" or "IR-SPA-ME/SE class"?
When the licence was re-printed, did the entry change affording you SE IR privileges?
I'm probably giving the CAA too much credit, but I don't think their computer would allow them to issue the "SE IR" element without the relevant class rating. The rule implicitly requiring the appropriate class rating came in fairly recently so they should be looking for it.