This is a very interesting thread, so I thought I'd throw in my quarter, too. Understand what I am saying is mostly from my own experience or what I remember hearing and reading.
One woman, April, posted early on, "I *think* I recall that site specifying that the tiny tongue sores are caused by the same virus that causes cold sores on the lips or around the mouth, and the sores like the one you have on the inside of your lip or cheek are something else."
In the mid-90s I was having quite a time with this tiny little bumps on my tongue, little patches of them that were really really painful. Someone told me the same thing, too, that they came from the same virus as cold sores (which is Herpes). I want to stress, it was heard as hearsay and I can't remember if a doctor told me this or if a lay person did. I assumed it was correct because I knew I carried Herpes. I had also "heard" that canker sores on the cheeks and gums are from something else.
I want to bring up Herpes, and you'll see why as I read on. In the late 1990s, I read in "The Helper," a newsletter for and about Herpes, the following, and I'm paraphrasing. This may or may not be related to the original poster's complaints, but because of the severity of it and the little bumps on the tongue, I thought I would mention it.
It said that a person can "carry" Herpes I or II in either the nerves near the neck (mouth) or pelvis (genital area). Depending on where one contracts either virus depends on where, how often and to what severity the Herpes type will manifest.
Herpes I (HSVI)'s home is in the nerves near the base of the neck while Herpes II (HSVII)'s home is in the nerves hear the base of the spine (or pelvis). That's why most people think when you get cold sores in the mouth you have HSVI and when you get an outbreak in the genital area, you have HSVII. But, that is not always the case. If someone contracts HSVI (common cold sores in the mouth) through oral sex on the genital area, that person may have a breakout in the genital area once or twice in their lifetimes, very mild. If someone contracts HSVII through oral sex in the mouth, that person may have continuous severe outbreaks of cold sores and other sores, very severely, in the mouth region. I think there are reasons for these differences, such as different behavior when each virus is located away from it's "home," but I believe another reason for the difference in severity is that HSVI is a milder strain of HSVII. (Normally, HSVI in the mouth area would produce mild occassional sores while HSVII in the genital area would produce severe outbreaks in the genital area. With it switched around, the severity of each strain is maintained, maybe lessened somewhat because of being away from it's "home," but just located in different nerve regions).
A good, close friend of mine had one outbreak in the genital area in 1992 and was devastated. Her doctor told her that she had HSVII. But she has said she has never had an outbreak since. She had a period of time in the mid-90s when she was having these little bumps and clusters of tiny sores on her tongue. She never got cold sores on her lip. Anyway, they were aggravated by drinking orange juice and eating oranges, limes or lemons. She started taking a multi-vitamin and L-Lysine, as some people have already mentioned. She hasn't had any symptoms since the mid-90s.
She got a blood test in 2000, which showed that she was negative for HSVII and positive for HSVI. The mild contractions in the mouth and genital region suggest that this person does have the milder strain, HSVI, and it could be possibly located in both the nerve areas of the neck and pelvis, even though she experiences no symptoms now.
So all I'm saying is to ask for your blood to be tested for herpes, both strains of it. If you have HSV type II away from its "home" at the nerve base of your neck, you may be experiencing these sore outbreaks due to that virus (because it is a stronger strain). The other possibility is that your immune system may be so broken down that HSVI (a milder strain) maybe be manifesting more powerfully due to your immune system breakdown. That's why a blood test will clear it up.
Oh, and even if you keep track of your sexual history, even if your partner says he/she is clean, even if you do everything "right," one can still contract Herpes, either type. People even give it away without knowing that they have it, some don't have symptoms, their immune systems are so strong that there is nothing, not even cold sores. That's why it's important to know whether or not you carry it. I also had a friend who said that it's possible for mothers to pass either strain of the virus onto their children when they are being born, sometimes unknowingly. That's why sometimes kids can get sick with it when they are young.
And all this, of course, based on whether or not the little tiny bumps on the tongue are part of the Herpes virus (of which I am not 100% confident). I suspect that there is a bigger problem going on, something with the immune system, so that's why I 100% support all the comments about boosting your immune system now, irregardless.