Balance Initialization process run for New Secondary Ledger and has balance variances b/w PL and SL

Summary: We are creating new secondary ledger for existing primary ledger and we were trying to use the functionality of balance initialization to initialize balances in new SL to match the ones in PL. The standard process was run and now we find huge balance variances between both the ledgers in their TBs for the initialization period.

Content (please ensure you mask any confidential information):

1. We were of the understanding that the balances will be matching between PL & SL after the process is run but since that is not the case, what might be the reasons behind the same (apart from the one discussed in pt 2)?