How many sub-grids are attached to your ship? Sub-grids are the grids connected via rotors, pistons and hinges. The only way to get an accurate block and PCU count is to attempt to copy (CTRL+C) the ship and see what the block count and PCU count is before you paste the copy into the world. There should be some information at the bottom of the "ghost" version of your ship you're about to paste.

Another issue maybe be projectors with cached projections in them of grids with cached projections in them etc. You may have a Russian-doll effect of extra blocks being counted due to projectors.

Make sure your ship isn't docked with a station. Made that mistake a time or two myself...

Does it have a projector on that has an active projection on?

^^ What @Governor said, I'd lay long odds you've got a self-repair projector and have been several rounds of replacing the self-repair projection with the latest version.

The always-blueprint-just-one-level dance is full of these annoying little steps to get the truncations applied in the right place:

1. "Remove" the current blueprint from the self-projector.
2. Copy the build.
3. Replace the blueprint with that copy.

The most counterintuitive step, have faith:

4. add the blueprint with the empty self-repair projector to the self-repair projector.

5. copy this new build with the wonderfully-amnesiac history
6. Replace the blueprint *again* so when you use it you get just the one level of history in your repair projector.