What happened to Ichigo in Urahara's training area after meeting Byakuya (for the first time)?
It's pretty simple. When Urahara starts training him, in the end of chapter 60,


   Tessai breaks Ichigo's Chain of Fate. Urahara explains that the corruption of the chain has already begun, and when it reaches Ichigo's chest, he will become a hollow. The only way to stop that would be to regain his Shinigami powers. Then they throw Ichigo into the hole, and seal him with bakudou 99. 


In the end of chapter 62,


   the chain corruption gets to Ichigo's chest, and he starts transforming into a Hollow - you can clearly see his mask appearing (though Urahara comments that the mask forming before body indicates that Ichigo is resisting the transformation). However, Zangetsu helps Ichigo to stop the transformation in the middle and regain his Shinigami powers. 


So yes, the reason is simply that 


   he was already half-transformed into a Hollow when he gained his Shinigami powers back and stopped the transformation.