My oldest (now 11 years) would wake up screaming. Here are some of the reasons:
1: Allergies -- he's allergic to milk. If I had any milk product, he would double over in pain later that day or night. If either parent has allergies of any sort in their family history, you may want to check this out. (My 3 kids have: milk, soy, almonds, rice, food coloring, dust/mold, and I don't know what else. We discovered most of these by observation: tummy pain, allergy ring around anus, diaper rash, eczema, etc.). Feel free to contact me if you have questions about allergies.)
2: He started teething at 3 months and kept a regular schedule of one tooth every two weeks or so. He had all his teeth in by 12 months. We ended up giving him Tylenol as needed at bedtime so we could all get some sleep.
3: Over-stimulation -- more than 1 hour of TV a day would make him "colic-y" all evening and waking up at night.
4: He needed to be outside at least 10 minutes every day or he would be cranky.
5: He went thru the "night terrors" phase in his second and third years.
6: Any time he was growing physically or developmentally, he slept poorly.
7: General illness.
After re-reading your email, my guesses would be to check for allergies, illness (fever?), gastric reflux.
Bottom line: if your gut tells you something is wrong, pursue it until it is resolved! Trust your gut! And hang in there!