I'm unable to reconcile the differences between R and BB accounts. What should I check to find the reason for the difference?

If you face issue regarding the difference between GSTR 1 and B2B Accounts then you can run one Utility that is Update Voucher GST Summary and for this you can follow some steps: 
 Step 1- Take the backup of your concern company. 
 Step 2- Open your company and go to house keeping 
 Step 3- After click on house keeping Click on the Update Voucher GST Summary. 
 Step 4- Click on the partial or can select full and run the process. 
 If issue persist then You can follow another alternate and steps are: 
 Step 1: Go to the Display and click on GST reports . 
 Step 2: Now click on GST Audit Reports and then click on Reconcile Accounts and GST. 
 Step 3: Now click on Sale for reconciliation and specify the time period. 
 In this report you can check your data as per GST and what you have entered in BUSY and correct those entries. 
 If issue persist then you need to check month wise by enter date then you will get period in which mismtch will be exist and then you can check in short range of date within that mismatch period and then at last you will find the date where mismatch is heppening then you check your entries and rectify them.