you have to make sure that Giga and Cubase do _not_ use the same physical outputs. If the ASIO-driver (Cubase) e.g. uses the outputs 1-8 (ADAT1), then you can\'t use these with the GSIF-drivers in Gigastudio. Use 9-24 instead.
Don\'t know if you\'ve solved this, but I had similar problems until updating to Cubase 5.1 and Gigastudio 2.5. Now everything seems to work OK - eaxtly as you would expect it to, although I haven\'t given it a real hard working to yet.