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Sorry to hear you are having issues with the NY IT-204-LL payment form. Let me see if I can help you through your issues.
This calculation in the software needs to have a few inputs by the user in order to calculate the appropriate payment amount. First please review the section of the form above Part I: General Information. Is there a checkmark indicating if the entity is a general partnership or limited liability company (LLC)? If no checkmark is transferring then the program does not know what kind of partnership and what fee to assess on line 5 of the form. Review your entry on the federal Form 1065, page 2, line 1 to ensure the type of partnership has been entered.
Now let's assume you have a checkmark indicating this entity is a general partnership. If the user also checks yes to question 1 on the IT-204-LL and the entity's gross receipts are over $1 million on line 4, then a filing fee should populate on line 5.
If we assume that the entity is an LLC or LLP and the user checked yes to question 1 on the IT-204-LL, then the filing fee should populate on line 5. You should ensure gross receipts on line 4 are entered to be sure they correct fee is being applied.
Finally if we assume that the entity is an LLC or LLP and the user checked the disregarded entity box underneath the LLC/LLP checkbox, then the user would need to enter an EIN on line 6 of the form. Once the EIN or SSN is entered, then the filing fee should populate on line 7.
Hopefully this is helpful.