In general, if there is a smell, something is wrong.
What kind of smell are you experiencing?
Now if you have a really sensitive sniffer, make sure you are not simply smelling the fish food.
Are you growing any plants with a strong odor? Some people might not enjoy growing indoor onions.
What do your water tests say? This is the big one for determining if you have a good balance.
What type of system is it? Flood and drain? Constant flood media? Raft? NFT? Something else?
Only places I've really experienced problematic odors from an aquaponics system have been when I tried NFT without filtering the water first (the fish poo would build up against the plant roots and become very nasty, I mean gag a person with a really strong stomach nasty.) Or if you are doing constant flood media with very minimal flow, especially if the top of the gravel is wet and growing lots of algae, sometimes that will give a stronger odor that one would like indoors.
And the most likely area where you would run into an issue is if you don't have enough flow and aeration, anoxic or anaerobic areas in a system can give you quite the "pond bottom" odor so for an indoor system you will want to make sure you have plenty of flow through your tank and beds and if that isn't keeping the pond muck odor away you might need to add supplemental aeration.
It smells like you have something fishy going on...
Nitrites at 10 ppm??!?!?!?! Are there any fish in there? eek
With the Nitrites high, perhaps you did just get past the ammonia spike.
45 gph probably wasn't enough. Hopefully with the bigger pump now things will be better. I would recommend having some air movement like a small fan which will also help the plants in an indoor set up.
ok, had me worried.
changing to water in your system would set you back to the beginning. remember that your system will have hardly got working (nutrient cycling) at this point in time. not sure what your system is like but it could be not enough bio-filtration and your water cycling speed is incorrect. do you have some dead fish somewhere? lastly, what is your storage medium? i have come across totes, plastic barrels and containers that smell really strong & bad.