The sugar content is fixed between your frozen vs. fresh fruits, right? The only variables you have here are 1)temperature and 2)something maybe less obvious on the surface. One food is cold and the other is room temperature. The second and more elusive variable is water content. The frozen food contains a much higher level of H2O.

Let's ignore temperature and focus on the H2O variable. Water happens to be a byproduct of glycolysis, or the breakdown of glucose (C6H12O6) to make ATP. The primary waste byproduct of cellular respiration is CO2.

This YouTube explains cellular respiration (Glycolysis, Kreb's Cycle, Oxidative Phosphorylation):

Click here to watch a cell break down sugar

When you convert sugar/glucose (C6H12O6) to make ATP + CO2 + H2O you want your cells to be fully hydrated or balanced with H2O. At worst, if you do not have enough H2O to balance out the CO2, your body will attempt to acquire more O2 and you will hyperventilate (breathe in too much O2 and get rid of too much CO2 too quickly). Your body is just trying to balance PH because excess CO2 makes the blood more acidic.

Can H2O help buffer the blood? Of course. You can use the oxygen atoms from H2O molecules.

Blood PH

Excess CO2 may be causing the symptoms you describe. I suspect your level of dehydration factors into your body's differing responses to consumption of glucose in fresh fruit vs. glucose consumption in the form of frozen fruit with higher H2O content.

In your daily life, it's possible that you do not drink enough H2O, drink too much caffeine or both.

Headache, muscle cramps and panic attacks/anxiety are all conditions present where there is an excess of CO2 and lack of adequate water buffer to balance blood PH.

To test my hypothesis, try drinking a glass of distilled H2O 1 hr prior to consuming the glucose in fresh fruits. Bump up to 2 glasses of H2O, 30 minutes before eating fresh fruits. If the extra hydration has no effect on your symptoms then I am wrong (probably the case because I'm still studying basic science courses). If hydration does reduce symptoms, then H2O is at play here and I win the bounty!!!!

Maybe you don't have to say goodbye to fruit? Maybe you just need to say hello to more H2O?

My guess is histamines. Freezing grapes must destroy, make dormant, or minimize whatever is causing the allergic reaction to the fresh ones.

I first noticed this effect when I was a child. Fruit was supposed to be good for you, but trying to just fill up on fruit tended to make my head hurt and I'd feel a bit like I had hayfever. I've also had histamine responses to exercise when I was younger. I have been eating frozen fruit this summer and I haven't noticed a reaction at all.

wikipedia's Histamine page

Since the sugar is the same in both cases, the logical thing to do is look for some other factor.

Since you noted it didn't happen before paleo, is there a chance its a psychosomatic reaction? I think our minds play a huge role in how we react to foods. If I have some sugar but I'm completely ok with it and enjoy it, I won't really feel much worse. If, however, I regret it, then there's a good chance I'll notice some unwanted effects. I also remember Kurt Harris talking about one patient of his who convinced herself she could eat only chicken breast and oatmeal (or something like that). Anyway, just something to consider.

I wonder if freezing shifts glycemic index and changes digestibility. I dredged glycemicindex.com for a comparison between fresh grapes and frozen grape juice, but found nothing. However oranges are well covered. It looks like going from fresh fruit to frozen juice increases the index by about 20%. I'd postulate rupturing/removing the juice sacs aids digestibility. The sugar is thus more accessible after freezing. In the bad sense freezing causes more of a blood sugar spike, but in the good sense it passes through digestion faster.