When search-for-xlinks enocunters a tie in XCorr score, it reports both matches. This is correct. However, the delta_cn values are different. In this file:
the first two lines correspond to matches to scan 22. Both have an xcorr score of 0.039691944, but the first has a delta_cn of 0, and the second has a delta_cn of 0.00029008836.