This is normal. The spreads function works on a per-file basis, so any single pages in a doc export as singles in the PDF. I would export without the spreads checkbox, then use Acrobat to set the initial view to two-up with cover.
The larger question in my mind is why you want to export spreads...
my boss likes me to to export spreads for the higher ups as they aren't to savvy with page display in acrobat and will not know how it looks in spreads otherwise
i already knew i could do that in acrobat, but i needed it to be actually exported as spreads
You can set the initial view so it opens as spreads, and if they aren't savvy enough to know how to change a view that's all they will see.
Beyond that, the only way you are going to get spreads to export as doubles thoughout a Book is to move pages from chapter to chapter to make all chapter start on a left page and end on a right.
You can use a multipage importer to import a single Page PDF into InDesign.
Create a single page PDF
Create a facing pages document the same size as your original file
Multi-page place the entire pdf into facing pages (automatically done by script)
Export entire book to PDF as spreads.
I say to do this with a singe pages PDF - because I don't think it will import multiple InDesign files, you'd have to place them individually - and with my experience it takes longer to import multiple indesign files - so I just use a single pages PDF.
And just to note - I do this with a magazine where all the articles are individual InDesign files (currently I have 46 files in this magazine) - and I use the multipage place an entire pdf into a new document so that I can use the File>Print Booklet Feature.
One more downside to exporting spreads is that you can't use the Go to Page ___ function. For example, if you want to go to page 31, you have to tell it to go to the 16th spread. Since they can't figure out how to view as facing pages, maybe they don't know they can go to a specific page either.
My way will fix that
I didn't mention this method yesterday because, frankly, I don't think it's worth the time and effort just to show a screen proof to people untrained in the use of the page view controls in Reader. If they don't know how to set the controls themselves, they aren't going to mess with the initial view you set.
Ah yes - it's a good point.
From my experience someone will try fidget around with and it will go haywire. Best to show it to them the way they ask for it - and InDesign doesn't have the feature necessary to get something that should be simple.
Anyway - there's a few options for the OP and hopefully that Page numbering thing will be fixed if they import the entire pdf into a new doc and export it again as spreads.