The issue with the Clipper that was causing this problem has been fixed in FME 2018,which can be downloaded from www.亚搏在线safe.com/download.
Looks like this is a known issue (PR#77325).Where the nodata is set to NaN (Not a Number) then there is a problem.As others have suggested,using a RasterBandNoDataSetter to change the Nodata value to an actual number is a good workaround.
If you need to follow up on this,contact our support team and let them know it is related to PR#77325
As@zzupljanin,mentioned,you can try adding a transformer before clipping.Another option would be theRasterBandNoDataRemoveror theRasterInterpretationCoercer.If you can attach your workspace and sample data,I can try this out.
Interesting,did you try to use RasterBandNoDataSetter before clipping