I had the same issue with purchasing the NX from the c-store. The only way i could manage to make the transaction work was by changing to my main character and emptying a ship slot on his roster, even though i was puchasing the ship for my alt.
Next I changed over to my alt character and purchased the ship. Transaction went smoothly... hope it works for you, sounds just like the problem I had.
Here's the only things I know about the c-store.
2: Ships can't be purchased if your ship inventory on the character is full. If you have 8 ships the game won't let you buy another ship until you delete one or purchase more ship slots.
hmmm, I never knew that, maybe that is why I cant purchase my excelsior....
hang on, scratch that, cos when I go to the ship store, I can still buy lower ship tiers, its highlightable, except with excelsior, its not ?
If the T5 Excelsior isn't highlighting it almost always means the character trying to purchase it is too low in Rank to do so. I know the ship can be unlocked for play at RA but you might possibly need to be RAUH or even VA to purchase it. That I don't know, as I purchased mine from the C-Store with my VA when it first came available. If you have a Federation VA I would try to do all my buying with that character. If VA can't buy it, and he/she has an empty ship slot, then I would suggest you submit a ticket as there might be some type of problem with the C-Store.