I believe I see the problem. You are using a starting mobile phase (mobile phase A) that's nearly 100% ACN and a final mobile phase (mobile phase B) that's aqueous, and then generating your gradient by blending these two solvents. That is a bad idea for the following reasons:
1) As you've learned, 100% ACN is a poor solvent for electrolytes. It's also a poor solvent for B vitamins.
2) The mixing of water and ACN is an endothermic reaction; the combined solutions cool. This change in temperature could affect the chromatography. You would be better off having some water in the mobile phase A reservoir along with the ACN and having some ACN in the mobile phase B reservoir along with the water. Ratios of, say, 9:1 or 1:9 would suffice. That way, the endothermic reaction takes place prior to the chromatography and you can use mobile phases that are at room temperature.
3) It isn't necessary to use high levels of ACN in order to get B vitamins to be retained adequately in HILIC, per the following example:
http://tinypic.com/view.php?pic=287hyl1&s=9
To spell out the running conditions:
Column: PolyHYDROXYETHYL A, 200x4.6-mm, 5-µm, 60-Å
Mobile phase (isocratic): 40 mM ammonium acetate, pH 5.0, with 75% ACN
Flow rate: 1 ml/min
Detection: 265 nm
Retention times: riboflavin (B2): 3.6'; pyridoxal phosphate (B6): 4.8'; thiamine (B1): 9.5'; niacin: 13'.
Thiamine pyrophosphate will be even better retained.
You should make sure that you have at least 20 mM salt present in order to shield negatively charged groups in the vitamins from electrostatic repulsion, since most HILIC materials have at least some negative charge.
If you start with, say, 80 or 85% ACN in mobile phase A, then you will have adequate capacity for dissolving enough salt in it to serve your purpose. It is important to use this as the sample solvent as well, or at least a solvent that has the same concentration of ACN to within 10% of that in the mobile phase. Otherwise, you could get skewed or even multiple peaks for your analytes due to "fingering effects".