Stratix II GX serdes synchro problem

You should read the Handbook section on this: http://www.altera.com/literature/hb/stx2gx/stxiigx_sii5v2_01.pdf, specifically 2-80 and 2-81. The rx_bitslip signal is active on the rising edge only, one rising edge one bit slipped. Pg. 1-6 of this document goes over the supported modes of the Word Aligner. It seems with a 10-bit pattern you could use Manual Alignment, using rx_enapatternalign, rx_syncstatus and rx_patterndetect.