I've now got a second big-cryer-baby. Phoebe doesn't cry as much as I remember Natty used to, but yes, there are times when she'll cry and cry and it seems there's nothing I can do for her.
By all means, check things out. I took Natty to the dr about it because it seemed to be happening all the time. The dr recommended giving Panadol and seeing if it had an affect (Panadol isn't a sedative, so if bubs stops crying you can assume they were in pain, KWIM?) but it did nothing for Natty - she just needed to cry. Once she was 6-ish months old she became heaps more settled and happy.
With Phoebe, I just assume that it's tiredness. Particularly if she's flailing her arms about the place. And even if she's just had a nap. If she is crying 'excessively', I wrap her up tightly and rock and shush her.
I hope you find some answers soon - crying babies are very tiring.