She is probably lethargic and having swim bladder problems because her water is cold. You really, really need to get a good reliable heater like this one: http://www.fosterandsmithaquatics.com/product/prod_display.cfm?c=3578+3743+11368&pcatid=11368
because temperature is essentially what drives their entire metabolism. Lower temperatures can slow digestion, circulation, and have a negative impact on the fish's immune system.
Could you give us any more specific readings on your water parameters? Do you know for a fact that your aquarium is cycled? You said you only recently started adding the tetra water conditioner, did you add any form of dechlorinator before you started with this? Does she seem bloated to you?
If the tank is cycled, you will not want to lower the water level too much because you'll starve the bacteria in the filter if the water cannot flow through it properly. You could put her in a plastic container with some small holes in the bottom and latch it onto the side, this way she has the benefit of the filtered five gallon but doesn't have to struggle to reach the top.
You should also consider making some drastic changes to her diet. Flakes don't have a lot of nutritional value and can cause bad cases of bloating and constipation in bettas. A high quality pellet food (Omega One, Atison's, Ken's betta crumbles, New Life Spectrum) supplemented with live and/or frozen food is a much better diet. Freeze-dried foods would only make her worse. Bettas and other fish were not made to digest dry air-filled food. If you use dried foods and especially freeze-dried food, you must fully rehydrate it in tank water first. Frozen and live foods (self cultured or purchased from a reputable source) are always better.
A heater and more frequent water (weekly) water changes should help her perk up quickly. Changing her diet should help keep this from happening again. Do not try to treat her with medication or antibiotics, this will likely only make the situation worse. If you think she's bloated, we can give you information on how to treat the problem using Epsom salt (magnesium sulfate).