Hi, my 6 year old daughter was also diagnosed in September and funnily enough experiencing the same thing, she often say she has a swirly tummy but when we check her she is fine, she's also getting upset about it. Im no expert but if their levels are OK, it must be hard for them and the realisation kicks in it is going to be every day for life, throw in going to school, highs and lows it's probably exhausting. Do you think he might be getting anxious about things?
Has your son seen a child psychologist? I don't know how it works in different areas but our nurse sent us to see one when our daughter was first diagnosed, I'm going to make another appointment as my daughter is finding things hard at the moment (she cut her leg when injecting and gets upset about it now) so I'm putting the low mood and stomach pains as worry.
Like I said I'm not an expert just what's going on with us and it might be different with your son, it won't hurt to mention it to the Dr or your sons diabetes team that's what they are there for to help.