I've done more testing and narrowed it down to one table that doesn't calculate SQL correctly.
Test 1: Works
SELECT ID
FROM TroubleTable
Result: 1,2,3,4,5
Test 2: Doesn't work
SELECT COUNT(ID)
FROM TroubleTable
Result: ?
I then Copied the table and filled my copy with test data.
Test 1b: Works
SELECT ID
FROM TroubleTableCopy
Result: 1,2,3,4,5
Test 2b: Works
SELECT COUNT(ID)
FROM TroubleTableCopy
Result: 5
So my question would be, what can cause a table to behave this way, but a copy of the table works as expected? Is it an indexing issue? Is it a possible sign of corruption?