Hi Akoumjian,
The way the estimate screen handles saving custom field values is reliant on first retrieving an Estimate # from QuickBooks.
At present, in order for a custom field value to be saved correctly, an estimate record must have an estimate # associated with that record. The catch 22 here is that Method pulls this Estimate # value from Quickbooks, which naturally cannot happen until you save the record and sync with quickbooks. You will notice that creating a new line item works, but under the "estimate #" column, no number will appear.
For the time being, there is a workaround. When creating a new line item, hit save before entering a custom field value. Then refresh on the left-hand side to verify an "estimate #" has been assigned to the record, and return to that record to enter any custom values, and then click save again. The value will now be retained. I have filed a bug report with our developers, and as soon as this issue has been resolved, we'll update this post.
Regards,
Denis