Of course, otherwise there's no point in a forum

I guess it just goes to show not all Business Class fares are equal. Not all I class / R class fares are even equal. In future ask the travel agent to compare published fare (use this exact phrase) against the company negotiated fare and see if there is any difference. Perhaps get them to quote the negotiated fare first before asking for the comparison to make sure they do not make make the company negotiated fare look better than it is. If your company culture allows or encourages it then it might be a useful conversation to ask your company travel manger what their travel policy is. If there is a kick back to the business buying one fare type over another. This might provide more background to the story over why you have to book travel in a particular way.

Anecdotally it is possible (or at least it used to be) to upgrade using Avios on the day at the airport. Although the on the day price was significantly more than securing from Avios availability in advance. This may still be an option on the day so worthy of asking at check in if any upgrdes using Avios are possible.