homemade primers and new kits

[secundo]

Has anyone had trouble using homemade (i.e. non-illumina) PCR primers over the past few months?

We use our own (unmodifed) oligos for PCR amplification of libraries. This worked great about 8 months ago, but over the past couple of months, our cluster generation has been terrible. This change coincided with the kit and flow cell upgrade, and we wonder whether this is new chemistry that requires the use of Illumina PCR primers with all of their semi-mysterious modifications (phosphorothioate linkage, and perhaps others).

I'd also love to know exactly how these primers are modified, if anyone knows.

Thanks!!