Need a few more details, but my off the wall guess would be just color profiling issues.
What software are you using and what formats are you exporting to? Oftentimes I will export EPS from Coreldraw. If I need exact colors, I will use my pantone chart, if I'm kind of going for a photograph/raster style with drop shadow effects and the like, I'll usually convert to an RGB bitmap first, then export to EPS.
Does this problem affect old artwork/jobs?
If it doesn't, it's definitely a software related issue. If it does, then a few things could've possibly changed with the system setup.
Is the problem constant, or gradual (IE, starts red, then goes orange, then straight yellow?)
If it's gradual I'm sure someone with more Roland tech experience than myself will guide you through the troubleshooting process for that.