Unless the road bike isn't the size you need, it may just be a matter of getting used to a different position on the bike. I rode mtn.bikes for approx. 35 years before owning a road bike. Luckily, I bought it from a knowledgeable and very helpful bike shop. All they did was to put a shorter stem on it to make a more comfortable fit. Now, I was 55 when I bought it and was most likely used to the more upright position, if I had been riding road bikes prior, maybe it would have been ok with the stock (longer) stem. I still ride on the hoods on the road bike, still don't like being too leaned over. I have gone through a number of saddles, the one now is fine, some were torture devices. Different leg muscles are used also (at least in my case). The riding I do on my mtn.bike has me off the saddle most of the time. On the saddle while on the road bike.
Probably just an "adjustment" phase, assuming the road bike is the proper size for you.