Confusion about charset for connected tables from MS Access
I'm going to guess that the problem might be the difference between your table collation and the data_charset. Maybe try using a compatible collation, so how about this? Use CHARACTER SET cp1250, COLLATE cp1250_general_ci: 

CREATE TABLE pohoda.xfa (
  ID INT(10) NOT NULL,
  ... list of fields
)
ENGINE = CONNECT,
TABLE_TYPE = ODBC,
TABNAME = 'Fa',
BLOCK_SIZE = 10,
CHARACTER SET cp1250,
COLLATE cp1250_general_ci,
CONNECTION = 'DSN=pohoda_64b;DBQ=c:/path/to/mdb;';