Hello, my name is***** and I have over 20 years of experience as a veterinarian. I am very sorry to hear about your girl's apparent intermittent discomfort.
Even though she is an indoor cat allergies are possible, and allergies are the most common cause of itchy, uncomfortable skin. Flea allergy is the most common allergen and this time of year fleas have had all summer and fall to breed so they are at their peak levels, hitching rides in through screens and doors is common. Flea allergy seems to affect the tailhead and back area most so it is definitely possible.
I'd use flea protection every 28 days. Both Advantage II and Frontline Plus work quite well at killing fleas and are less likely to create a skin reaction.
Other allergens are inhaled (like mold spores or pollens) or food allergies.
To treat her allergic reaction to the flea bites (or any allergy) I recommend antihistamines and omega-3 fatty acids. Some antihistamines to try are:
1) Benadryl at 1mg per pound or 1/2 of a 25mg tablet per 10 to 12 pound cat 2 to 3 times daily. You can crush the pill up and hide it in something tasty like her canned cat food or you can give it directly. Make sure whatever you use is Benadryl only as the combination products with decongestants and acetaminophen are toxic to cats.
2) Chlorpheniramine 4mg per cat once or twice daily.
3) Zyrtec (Cetirizine hydrochloride) at a dose of 5 mg per cat given orally every 24 hours. (Make sure it is NOT the formulation with a decongestant (such as Zyrtec-D) because cats cannot tolerate decongestants.)
Omega-3 fatty acids will work synergistically with the antihistamine to soothe her itch and as a bonus will improve her hair coat and skin condition in general. I like the products by Derm Caps or 3V. These come in pump form to put on the food or you can puncture the capsules and dribble it on her food.
I recommend a dose based upon the EPA portion (eicosapentanoic acid) of the supplement as if we do that the rest of the supplement will be properly balanced. Give her 20mg of EPA per pound of body weight per day. For example an 8 pound cat could take 160mg of EPA per day. Antihistamines and omega-3 fatty acids work synergistically. These should help reduce the itch. Be aware that antihistamines can cause drowsiness or hyperactivity which should resolve with continued use.
Another possibility for her discomfort is a condition called hyperesthesia. Hyperesthesia is a poorly understood syndrome which is difficult to diagnose. These cats have pain and hypersensitivity to touch on their back and tails. They sometimes will bite at themselves because they are so uncomfortable. It is a poorly understood disease process with no definitive test for diagnosis and so other problems (such as spinal arthritis or infections or allergic reactions) should be ruled out first. We do know that stress does seem to make this disease process worse or flare more frequently. Sometimes mood altering drugs and steroids can be helpful.
Here are a couple links discussing hyperesthesia syndrome if you are interested: http://www.veterinarypartner.com/Content.plx?P=A&A=1998&S=4&SourceID=62
Another condition which initially causes pain, but can later lead to urine and stool incontinence is lumbosacral stenosis. This is a narrowing of the bony canal that the spinal cord travels through, either due to weak ligaments holding the vertebrae in place or arthritis changes in the vertebrae. It is more common in dogs than cats but it can occur in cats.
Has she has ever had radiographs of her spine?
Finally it is possible that he has a slipped intervertebral disc (the soft cushions between the vertebrae which allow spinal flexibility). When this happens pressure is placed on the spinal cord which is quite painful.
If she has ever taken a fall or had some sort of trauma where her tail got caught and the nerves were stretched this can cause these sorts of symptoms too. As the nerves regnerate there is a tingling, sometimes painful sensation which can lead to the cat chewing or biting at the area.
LS stenosis and a slipped disc can be diagnosed with regular radiographs sometimes but many times an MRI or myelogram (dye study of the spinal cord space) is needed.
Anyway in your cat's case I would start with trying to control allergies and if that doesn't work then she needs a thorough examination, as well as bloodwork to make sure internal organ function is normal, and a urinalysis with culture to look for a urinary tract infection, as well as radiographs of her pelvis/spine. If that all looks normal referral to a neurologist for an MRI may give you the answers that you need. So yes, she may need an exam, but there are a few things that you can try at home first.
Let me know if you have any further questions.