G/L accounts are not configured on Flow type level, this is done over the whole chain (as you might know) Flow type -> Update type -> Posting specification -> Account symbol -> G/L accounts.
for some Account symbols, e.g. '3 - Bank clearing', some slightly different rules apply, when the Account symbol is not assigned to some specific fixed G/L account, but kind of substitution.
there are also other settings, relevant to Payment process, though from your provided description I'm not able to guess if this is relevant to you or not - could you please confirm if the relevant Update type 'F1100' is relevant to incoming or outgoing payment?
Kind regards,
Renatas