The best option with regards to buying postage labels would be to bypass eBay altogether and purchase the postage labels from the Post Office. That way you can choose to buy whichever postage label you need to post out the items and won't have to put up with the endless problems caused by trying to purchase postage labels off of eBay.
With regards to posting the items to the buyer, you could send both items in one packet, despite the fact that the buyer has paid separately for both items. However, although you will be able to add the tracking number against one of the items, you will not be able to add it to the other item, so the best option in that case would be to contact the buyer via eBay Messages on the item that you have not entered tracking details against, saying something along the lines of "Thank you for your purchase. This is just a quick e-mail to let you know that both of your items have been sent together in the same package, and therefore the tracking number showing up against the first one is the same as the other item, for which I was unable to add a tracking number due to the fact that eBay will not allow duplicate tracking numbers to be used on two separate purchases."
In the event that the total amount of postage comes to a higher amount than you had to pay for the postage label to send both items in the same package, refund the balance to the buyer and add something about this to the buyer in the message so that he/she knows that you have issued him/her with a partial refund and are not trying to rip him/her off by pocketing the excess money from the amount paid for the postage.
In case you are still apprehensive about taking this advice, when I used to sell on eBay and found myself in the situation that you describe the solution that I have outlined above was something that I would do in order to resolve the issue, and I never had any problems from buyers as a result of doing it.
Finally, if you do decide to do as I have suggested, you will have to mark the second item up as having been despatched by clicking on the envelope icon due to the fact that you can't enter the same tracking number for two transactions that have been paid for separately. The transaction that you use the tracking number against will automatically be marked up as despatched as soon as you enter the tracking number and confirm the details.
