I read somewhere it's a problem with Seagate's 9 series onwards, there's difficulty in running 2 drives with them. I guess your Seagates are version 7 or 8?
Well now there's an interesting question. Someone on the NZ forums has done it I think, I'm not really sure on how to capture the IR codes either but I'll give it a go and if it doesn't work I'll "downgrade" from MySky to a standard decoder.
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