36 male, software developer... experiencing very deep funny feeling pain in middle toes when lying idle and and flexing the toes. what could be reason and how to ease it?

Nerve pain: You may have a pinched nerve. You should try back stretching exercises. If no relief is noticed in 2 wks, go to your doctor for evaluation of your back to see if you need to get imaging study of your spine to confirm diagnosis. Feel better:)

You have some nerve.: You symptoms and description of "deep funny feeling" sound like a condition known as Morton's neuroma. Without a hard exam, it is difficult to be absolute, but you can do a search and compare known symptoms and treatment protocols.