Ok here's the deal:
My office just got Acrobat X for our office
We use AutoCAD 2008 to 2010
If we plot a drawing using AutoCAD with the Adobe PDF plotter the drawing comes out as intended
If we publish a multiple layout drawing using a page setup that has the Adobe PDF plotter the drawing comes out as intended
But!! When we create a PDF of a DWG file through Acrobat X, if it's one page or multiple pages, it is created with the left and bottom edges cut off and the margins are offset from the page set-up. It must be some kind of paper size/ margin issue or maybe a postscript thing. I don't know. It's not AutoCAD as far as I can tell. I've dittled with every setting I could think of with no result. Please help. My company just bought each employee a license on my advice and they are very unhappy with this outcome.
Also,when I run a batch plot from AutoCAD teh same things. Moreover, some elements and layers don't even get shown.
There are some things to note however:
1) When batch plotting, you must set each layout's plotter to "Adobe PDF" first, then choose "Plotter from page setup". Choosing "PDF" from the batch plot dialog uses AutoCAD's internal PDF engine even if Adobe PDF is selected for each drawing, however using the Adobe PDF plotter in batch won't combine the layouts into a single document.
2) Using the Create from File button in Acrobat and opening a DWG, you have the options to select which layout(s) to print and what to do with layers, but the extents of the plot are taken from the last saved configuration in the DWG and can't be altered. If the layout isn't set to plot the whole page with equal margins, neither will Acrobat. When the conversion is started, Acrobat opens AutoCAD and sends it a command chain, basically doing what you'd do when batch plotting from the AutoCAD ribbon.
As in your case there are strange effects in batch plot, seeing the same thing in Acrobat's convert results is not unexpected. I would suspect that it's an issue with the file rather than with either application. Without seeing a copy it's hard to say anything else, but can you confirm the sample DWGs shipped with AutoCAD export properly through all three methods?