Hi,
you should not use BEX queries on top of BPC standard generated InfoCubes since BPC standard has a special logic to interpret and handle data that differs from BW significanty, e.g. sign logic for accounts, YTD storage (if used) or calculated members. Since all these things are not known in BW queries you may get completly 'wrong' data, i.e. result sets of BEx queries and e.g. EPM reports may be different.
You might 'emulate' BPC standard logic using special features of BEx queries but then you have to know what you are doing.
You should consider to use BPC unified if you want to use BEx queries.
Regards,
Gregor