SCORM activities set to open in the same window are displayed in a small unusable iframe that loads in the bottom left of the screen. The same result occurs regardless of the dimension settings applied on the edit SCORM activity page. To reproduce upload any SCORM package as an activity in any course using Moodle 1.9.x. Be sure that "Display Package" is set to "Current Window".
I tracked this down to some small changes that are needed in mod/scorm/player.php and mod/scorm/rd.js. I've attached my version of these files with the changes comments as #scorm fix on line 285 of player.php and //scorm fix on line 80 of rd.js. You can also read my comments on this thread http://moodle.org/mod/forum/discuss.php?d=112909.
I've tested the attached fix in IE8, Chrome and Firefox 3.6.12 browsers. I've also tested with the darkb, standard and funky_black themes. In all cases the iframe adjusts to the height and width specified, even on the smaller width of the funky_black theme the scorm module displayed the size specified.
Some additional thoughts - I've not tested it with a long table of contents. You will see a line commented out that sets the height of the TOC div. This is because some themes (darkb) don't respect the toc "on the left" position setting resulting in the SCORM iframe being push down the page equal to its height. I found commenting that out is better than leaving it but I'm unable to test it with a long TOC since all of my SCORM packages publish from Captivate with only one SCORM TOC menu item. I think this is a limitation of Captivate.