How do I "accept" transactions in the register?

It sounds like you have multiple problems.

First off if the transactions went straight into the register with the blue dot (you can widen the column to also see the text New) then "accepting" them has nothing to do with them not showing up in the reconcile window.

The reason they wouldn't show up in the reconcile window would be that you are reconciling to a date that is older than the transactions.  That can happen if you are reconciling to the online balance date, and that date hasn't been updated.  Not updating the online balance date when using Express Web Connect has been called out as a problem many times lately.  The online balance/date has never been 100% reliable, but it seem to be worse lately.  If you go to the Accounts Details -> Online Services tab you can turn off reconciling to the online balance and then when you reconcile it will allow you to put in a date and balance.

Next as @Sherlock points out you seem to have automatic entry on and you can turn that off using the procedure he points out.  But to use it for these transactions you would have to first restore from a backup before you imported the transactions.

On the other hand you might want to know the difference between the two modes.
With automatic transaction entry mode on the process is this.
The transactions go into the register and are marked with a blue dot or blue pencil (New and New Match).  You are suppose to review the transactions to make sure they are correct for the categories and such and then click on the blue dot to "mark it reviewed".  The blue dot will go away at that point.  Also changing the transaction in anyway will mark it reviewed, the same with reconciling a transaction.

With automatic transaction entry mode as you know the transactions don't first go into the register, they go into the Downloaded Transactions tab, and then have to be accepted into the register.  And of course you can't reconcile transactions until they are in your register.