You may need to provide some code segment to at least help us seize the problem better but based on what you have mentioned, it appears to me as all you need is to change
goptions device=java (or goptions device=javaimg) to...well basically any "img" format so bmp/png/jpg even pdf
goptions device=pdf;
Not all SAS/GRAPH procedures are supported by the java applet or activex control and since you use a pdf output with ods layout anyway, you lose the functionalities they provide when they are converted as javaimg or actximg. Thus, any image format as device= will let you achieve the same results.
The drawback is that if you were using the applet/object ATTRIBUTES= and PARAMETERS= options, you will need to trace back how to achieve the same result with SAS ODS options instead as those are obviously not supported by png/bmp/jpg/pdf or any other image device
*Edit - when using device=java javaimg activex or actximg for pdf output, the actx control/java applet are first used to generate the graphic and then the graphics generated by the controls are saved as an img format (typically jpg) and that image save is used to generate the odf pdf. If you look in sas help documentation index search GBARLINE and look for "ActiveX and Java support for", you will find that it is supported (most functionalities at least) by the activex device but not by the java device. If you had been using the attributes= and parameters= options, using device=actximg might solve your problem without having to convert all object-based options to sas/graph syntax options. At least assuming that most of their functionalities were developped with the same variables names and whatnot.
Vincent
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