To help you get the solution you're after it would be good to know what you are trying to achieve with the two separate drawings of the same assembly.
Once we know this, there's likely a good solution to your problem.
I don't know if any of these apply in your case, but they are worth mentioning.
A few tips and things to look for:
1. You can sort the BOM. I love this and use it all the time. It even saves the sort criteria so when there is a change you can just tell it to re-sort to get the list/order updated.
2. Check to see if items are included/excluded from the BOM. A lot of folks don't know about this, but properly used it is extremely helpful.
3. BOMs are tied to configurations so make sure the configuration shown is the same as the configuration referenced by the BOM.
HI I know about ordering BOMs and there is one configuration.
To answer Bjorns question, it is the nature of our assembly and how we have found it best to do our drawings that we have two drawings with the same final assembly. For the second drawing various items are hidden in the drawing (hide component command, not hidden in the assembly) I thought it may be due to me hiding components but it isn't. As a test I created an additional view with the final assembly , created a BOM from that view. There is only one configuration and I have gone through and made sure nothing is excluded that shouldn't be.
The fact is I will create two drawings, each with the same final assembly, however when I create a BOM in one drawing I have sequentially ordered numbers but when I create the BOM in second drawing I don't.