I can tell you definitively that he was horribly constipated throughout his life. He wrote and talked, with that German earthiness, about it to his disciples quite extensively blaming the devil/the pope for his trials. If you want to know more check out /u/bumbomachides comment below. As for dreaming up all of his ideas while sat on the loo, your teacher might be referring to the period when he was shut up in the Wartburg Castle for his own safety. He was essentially confined to a single room with a desk in one corner and, a bed in another and a chamber pot. It was during these few, constipation ridden and thoroughly stressful, months that he translated the New Testament from the original Greek and mounted attack after scathing attack on his theological enemies. There was also that little buzz in 2004 when archaeologists discovered the toilet that he probably used in the monastery in Wittenberg before the publication of the 95 theses.

German society in general was incredibly scatological in general -- it was just a part of the language of polite society. His chattering away about what colour his poo was this week wouldn't have been hugely noteworthy. In my mind though, what is more interesting is his identification of the devil as the cause of his pooping troubles. He genuinely thought that he was under constant spiritual and physical attack by popish forces which did not want him to spread his true gospel. The poo thing is part of this because of the way that he equates the devil with his enemies. So since the playground of the devil is the shitter, the same is true of his opponents. So he writes “Dear Devil . . . I have shat in my pants and breeches; hang them on your neck and wipe your mouth with them.” This view made its way into general reformation propaganda -- a set of woodcuts by Cranach the Younger featuring the Pope being shat on by three devils in hell comes to mind. Luther and most of the people around him were a bit poop obsessed.

If you want to know more Lyndal Roper talks a bit about Luther and poo generally in "Martin Luther: Renegade and Prophet". She also gave a lecture a few years ago solely about him, his poo and his dreams, although I'm not sure whether she published it. You might also check out Danielle Mead Skjelver's" German Hercules: The Impact of Scatology on the Image of Martin Luther"

Edit: It was Cranach the Younger, Not Duhrer. Creds to /u/Flopsweater

Who can offer an educated guess on the cause of his issues?

Is it true he ate spoonfuls of his own poop? My world history teacher told us that in 9th grade.