eps to pdf terminal switch messes up my whole image.

To be able to use transperency I thought it might be easiest and 
straightforward if I switched my output terminal from postscript to pdf. 

Unfortunately this messes up my graph almost beyond recognition!I've 
uploaded two (before / eps and after / pdf ) images here:

http://picasaweb.google.com/rpnabar/Debug_gnuplot_ps_pdf?authkey=
1OpZsQ7LhMs ( http://tinyurl.com/3lcsqz
)

 Did I set some settings wrongly? Or are these two terminals simply not 
****table? 

Old settings:
set terminal postscript enhanced eps color 
set output "scatter_plot.eps"
[snip]
`epstopdf scatter_plot.eps`



New settings:
set terminal pdf enhanced color 
set output "scatter_plot.pdf"

Other than these changes at the top of the script I kept everything 
identical.

If I made an eps and then used epstopdf on the Linux command line it gives

me a nice pdf.  Why does the internal gnuplot driver mess them up then?

Any hints for a quick ****t from eps to pdf? I only want it because 
otherwise I cannot use transperency. Will I have to manually redo 
everything?

-- 
Rahul