Sorry to hear about your symptoms.
It may depend whether you are peri or post-menopausal and how old you are? On the face of it, it sounds like something to do with the oestrogen dose you are getting and how you absorb patches and gel differently. What dose and brand of gel and patches have you been using? If you are still peri also, there will be fluctuations in hormones due to your natural cycle which will override the HRT and could cause the symptoms you describe. Nausea can occur with sudden high increase in oestrogen, like in pregnancy, but usually settles eventually. However if fluctuating then it will keep occurring with changes in your own cycle.
Hurdity x