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Hello, and thank you for your inquiry.
There are many reasons why people can have an eye muscle imbalance. It sounds like, from what your eye doctor has said (probably have had it for years), that this has been a hidden or 'latent' eye muscle imbalance which has been there in some small degree since childhood. At what age a person's eye muscle imbalance begins to decompensate is very individual--that can even occur much later in life.
Does your doctor suspect or did he do any tests to detect any medical condition that may have caused your eye muscle imbalance, such as thyroid dysfunction or myasthenia gravis?
It can take several days to adjust to a new prescription, especially one with prisms in it. However, I think two weeks should be the maximum time needed for adjustment. It is possible that your eye muscle imbalance fluctuates from day to day (that can be because of a disease called myasthenia gravis--which can be tested for, but the blood test can be falsely negative in those people in whom it only affects the eyes; but it also can fluctuate if your eye muscle imbalance becomes more pronounced with fatigue, illness, or visual inattentiveness.
Was double vision one of your initial complaints? Or was it just strictly dizziness and eye fatigue?
What do you mean by eye fatigue? Please describe the symptoms that prompted your visit to your eye doctor.
Are you near sighted (myopic = a minus in front of the first part of the glasses prescription) or far sighted (hyperopic = a plus in front of the first part of the prescription).
How many hours a day are you doing sustained near vision tasks such as reading or computer work and for how long has this been the case?
A phenomenon that can be found in younger individuals is something called accommodative spasm. This is a situation where the eyes spend so much time focused on near objects that the muscles that allow that near focusing start to spasm, which can cause headaches and difficulty changing planes of focus, such as when you're driving.
Often times people with this problem benefit solely from a dilated eye exam (the drops used to dilate the eyes can sometimes break the spasm). A refraction (test for glasses) should be done after your eyes are dilated and this can sometimes reveal a true glasses prescription which is less myopic and more hyperopic than what you're currently wearing because the accommodative muscles have been spasming for so long (it can simulate more myopia).
I'm not sure if your doctor saw that your eyes turned in excessively when you read and that's maybe why you have prism in your glasses, but if you do have some accommodative spasm and there is not a significant change in your refractive error even when measured after you're dilated, then putting a bifocal segment in your glasses may help with this discomfort and your visual symptoms.
Does this make sense and help to shed light on your concerns?
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DISCLAIMER: My opinion is solely informative and does not constitute a formal medical opinion or recommendation. For a formal medical opinion and/or recommendation you must be examined by your doctor.