Hello 
 
Carbohydrates can be unusually difficult molecules to chromatograph, as I have found out in the past few days in our lab.
I've been trying to separate glucosamine on a Kromasil NH2 column.  The Kromasil column is a new one and its performance checks out just fine, as one would expect from Kromasil.  The problem is not with the column, but with our method...and with carbohydrates in general.
Although NH2 columns are preferred for carbohydrates, they do need to be stabilised carefully before use.
In our case, we were getting a large peak early in the chromatogram, that we mistook for glucosamine.  The blank showed the same peak too, and we eventually realised that the peak was not due to glucosamine, but due to the sample solvent - water. Water interacts with an NH2 column, under certain conditions, and presents itself as a regular peak, when one uses refractive index detection.
The other problem was, glucosamine is highly water soluble and it elutes out rapidly, if we use water in the mobile phase.  So, we tried 100% acetonitrile, and we also tried phosphate buffers at various pH levels.  Retention times have improved somewhat but we're still working on the right mobile phase composition.
I'd suggest you equilibrate the column with the mobile phase for an hour at least.  Inject a solvent blank first to rule out ghost peaks.  Also, minimise water in the mobile phase, or if possible, do away with it.  Most carbohydrates are reasonably soluble in acetonitrile and methanol, so you can expect good retention times and separations, if you're lucky. 
If you need to use buffers, you might have to use a trial-and-error approach, as we did.  We experimented with KH2PO4 buffers, at pH 2, 4, 6 and 8, with various ionic strengths.
In our case, we think we're finally getting somewhere with pH 4, 50 mM KH2PO4 and acetonitrile (85% buffer: 15% MeCN).
I hope this is useful to you.
It's the simple molecules like carbohydrates that are usually the hardest to separate using HPLC - no UV chromophores, excessively water soluble, amphoteric, can't use gradients because of RI detection, etc..
Good luck.  
