"Under box 7 there is another box with a drop down but on my form, there isn’t anything applying to that second drop down box."
That's not relevant.
"I also checked the IRA/Sep etc checked as well".
That means both your pension and your IRA distribution were added together and placed on lines 4a & 4b. Go back and uncheck that box on the pension 1099-R (unless it is actually checked on the paper copy), so that it will go on lines 5a & 5b.
