Thanks everyone for all your input.
I have done what was suggested, that is, on the secondary I created  a new master key on the secondary, and created a new certificate from the backup of the primary cert.
As an extra step, and I don't know if this was required but it worked anyway, was that I removed the already restoring logshipped database that was present before TDE was turned on, and I re-established Logshipping from the primary to the secondary (this extra bit was done after I'd created the TDE configurations). What I did notice was that the database full backup that gets restored to initialise Log shipping (25Gb .bak file) did take considerably longer probably due to the overhead of encryption process.
Thanks for all your help guys.