Control read variation

[engencore]

We noticed a big difference in # of control reads between regions so we had our Roche tech out who said it was the PTP cartridge that was bad (installed for the Ti "update" in Dec 08). Since then, we see the same problem (i.e., large differences in controls reads between regions). Any ideas? We didn't have this problem until the release of Ti (Nov/Dec 08) and we see it on both FLX and TI.
Thanks for your input.
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Type Region Control_reads/region
FLX 2 12765/8030 (same sample in both regions)
TI 2 9187/5124 (different samples)
FLX 4 4694/3685/4382/3722 (amplicons of different samples but effectively the same)
FLX 2 6257/2906 (same sample in both regions)
FLX 8 1959/1941/2283/2473/1868/1518/1509/1837 (amplicons of different samples but effectively the same)
FLX 2 9356/8341 (same sample in both regions)
FLX LR25 1 region 5130
Ti 2 18314/99 (different samples)
FLX 4 16703/4789/1856/1073 (amplicons of different samples but effectively the same)