These are some of the issue for which probable solutions are given, hope they are helpful :

Scenario 1:
I have configured FBZP, Fi12 for house bank. But when I am doing payment run in F110 I am getting following error: 

Company codes X1YZ/X1YZ do not appear in proposal 05/03/2006 REMI2.

Diagnosis
No data exists for the specified paying company code X1YZ and the specified sending company code X1YZ in payment proposal 05/03/2006 REMI2.

System response
The payment proposal cannot be edited.

Procedure
Check the flow trace and payment proposal list in order to determine why the specified company codes are not contained in the proposal

Solution :
* That’s generic error for payment run, check whether there are any due items as on date (tcode fbl1n). You can also change the baseline date there and rerun it. if you still get same error.. Check the proposal log, you will find the reason.

* Try to see first whether any open items exist. By using FBL1N.

Scenario 2:
How to make the payment through automatic payment program, through F-110 .What are the prerequisites?

Solution : 
For Down payments to be paid using APP we have create a Down Payment request F-47.

Scenario 3:
While doing APP, after, " the payment proposal has been created message " if edit proposal is selected,  I am getting the error as "Company code ABC/ABC do no appear in the proposal "

Solution :
This type of error comes when your Payment proposal doesn't have any items to process. Check the parameters and ensure invoices are due as on run date.

Scenario 4 :
While posting customer invoice (FB70) why system asks for G/L account? As per accounting rules customer is debited and Customer reconciliation a/c is credited that ends double entry book keeping rule.  Why one more G/L account on top of Recon a/c, which is posted automatically?

Solution :
* Entry gets posted to Customer a/c through reconciliation account. You have to give a GL a/c for revenue.

Your entry would be 
Customer (Reconciliation a/c)    Dr
To Revenue                      Cr

* Reconciliation is a fictious entry so you cannot consider as an entry to be entered by the user. This rule is derived from the fact that 'we cannot enter/post directly to RECON account'. 

That is why system needs a GL account to make the account balance as zero.  Manual entry could be:

Customer a/c Dr
To Domestic Sales a/c
(Sales invoiced posted)

Recon entry is automatically made once you post this entry since you have configured your RECON in the IMG.

Scenario 5 :
I am unable to figure out how to attach my GL Accounts to my company code [copied chart of accounts, have my own company code, assigned my company code to the chart of accounts]. 

Solution :
You can attach the GL Accounts by just filling the details in the company code segment of the GL A/c. Hence you can use that gl a/c for your co code. 
But that would be individually creating the accounts. Right?? How about creating all accounts at one shot.   Create in FS00

Scenario 6 :
Difference between Standard Hierarchy and Alternate Hierarchy.

Solution :
Standard Hierarchy is basic structure of company but alternative hierarchy is just for reporting or temporary usage.

Scenario 7:
I have created depreciation keys (diminishing balance) and assigned to asset classes respectively. But at the time of asset master creation the system ask for Useful Life of the asset while my understanding is that in diminishing balance method there is useful life, just percentage is defined.

Solution :
Useful life is required for depreciation change. Normally a company with WDV depreciation may want to write off its assets which have crossed their useful life in 2 or 3 installments. This is achieved by depreciation change, where after useful life, a new method takes over.

Scenario 8 :
I have some conceptual problem in Internal Order.

Solution :
Internal order can only take a statistical posting & cost centre shall take a true posting when the relevant internal order is defined as statistical I/O IN T. code KO01(CONTROL DATA ) tab. So while making a posting in FB50 and assigning both I/O & COST CENTRE as relevant cost object in the transaction you shall get the stated status of these 2 cost object.

Scenario 9 :
In fb50, in the details tab, only if I tick 'calculate tax'  will the tax get calculated.
Our user wants this to happen always (by default), i.e. he does not want to tick this for each transaction. Is there any setup to be done for the tax to get calculated always?

Solution :
Even now you are not clear. T_Code FB50 is used for posting GL account only. I fail to understand how you can calculate tax which is generally from purchase / vendor or Sales / Customer oriented through FB50.

In case of local distribution, if we forget to pay taxes on certain items and we need to pass tax entries, then such a case is needed.  This can be achieved thru default parameter id for that particular user through transaction code SU3. 

In SU3, in Parameters Tab put "XTX" in Parameter ID column and in Parameter Value column put "X".

Scenario 10 :
We have an issue here where by the system is calculating the tax for an invoice with a wrong tax base amount. How do i change the tax base amount? I get the tax rates from VERTEX and they are showing right. Where does the system pull this tax base amount for an Invoice and how can I change it.

Solution :
Kindly check this:
spro - financial accounting  - f.a global setting - with holding setting - extended with holding  setting  --  calculation -- with holding tax type .

Check your withholding tax type, go in it and check the setting.

Tips by : Viji 

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