I have an 11 year old Longcoat Chihuahua that gives me a similar problem. We have 7 dogs and all of them will use a puppy pad but her. She was the first dog we had and we didn't start her on potty pads in the beginning and when we started getting more we introduced the pads. She will NOT use a potty pad. That seems odd to me since you would think she would WANT to pee where the others do, right? She is a marking queen outside but refuses to go on the pad to mark in the house. She also refuses to use the doggy door. She is timid about many things and even though we have a perfectly good doggy door where she could go out....SHE WON'T.
I really don't think she is the sharpest tool in the shed.

She only wants to use the bathroom outside or hidden down our hall. We realize that most of the problem is us because she does try to tell us but in her own quiet way. If we are sidetracked or she doesn't get our attention when it's time she just sneaks into the hall and piddles. We finally removed the carpeting and replaced that area with linoleum but it still irritates me! I have tried most things with her but to be truthful since we have such a housefull I tend to run out of steam and before I know it I am not so vigilant.
If nothing else....I feel your pain.