Some insurance companies seem to be pickier with the CCI edits then others.
According to AAPC Coder there is a CCI edit with those codes:
Code 99395 is a column 2 code for 90471 , but a modifier is allowed in order to differentiate between the services provided.
*Use modifier with code 99395
Note*: Always use modifier (if allowable) with column 2 code.
The current NCCI-associated modifiers are: E1, E2, E3, E4, FA, F1, F2, F3, F4, F5, F6, F7, F8, F9, LC, LD, LM, RC, RI, LT, RT, TA, T1, T2, T3, T4, T5, T6, T7, T8, T9, XE, XP, XS, XU, 24, 25, 27, 57, 58, 59, 78, 79, and 91. Read about modifiers for CPT and HCPCS codes
CCI edit Rule: CPT Manual or CMS manual coding instructions *
In the CPT book it states the "If a significantly seperately identifiable E&M service (eg, office or other outpatient services, preventative medicine services) is performed, the appropriate E/M service code should be reported in addition to the vaccine and toxoid administration code."
According to the above you are correct to submit them individually and I would try resubmitting with a modifier on the 99395 code. Unfortunatly, for coders it is a guessing game as to what the insurance wants as they will not usually give you the answer.
Let us know the outcome!
Hope this helps!
Amanda Kane, CPC, COBGC