Actually, I have the same problem still and I've installed the latest 3.0 stable release for the first time. The align and even vspace and hspace attributes do not keep when you add them in. The image properties box shows float:right or float:left but it doesn't keep.
I have to manually go into the the HTML view and modify it. But if I go back in to edit it again...just bringing in the HTML code to the box strips it out as well.
Is there a fix? Here's what my config looks like:
<!--
tinyMCE.init({
mode : "textareas",
theme : "advanced",
plugins : "style,layer,table,save,advhr,advimage,advlink,emotions,iespell,insertdatetime,preview,zoom,media,searchreplace,print,contextmenu,paste,directionality,fullscreen,noneditable,visualchars,nonbreaking,xhtmlxtras,template",
//plugins : "style,layer,table,save,advhr,advimage,advlink,emotions,iespell,insertdatetime,preview,zoom,media,searchreplace,print,contextmenu,paste,directionality,fullscreen,noneditable,visualchars,nonbreaking,xhtmlxtras",
theme_advanced_buttons1 : "save,newdocument,|,bold,italic,underline,strikethrough,|,justifyleft,justifycenter,justifyright,justifyfull,|,styleselect,formatselect,fontselect,fontsizeselect",
theme_advanced_buttons2 : "cut,copy,paste,pastetext,pasteword,|,search,replace,|,bullist,numlist,|,outdent,indent,|,undo,redo,|,link,unlink,anchor,image,cleanup,help,code,|,insertdate,inserttime,preview,|,forecolor,backcolor",
theme_advanced_buttons3 : "tablecontrols,|,hr,removeformat,visualaid,|,sub,sup,|,charmap,emotions,iespell,media,advhr|,print,|,ltr,rtl,|,template,fullscreen",
theme_advanced_buttons4 : "insertlayer,moveforward,movebackward,absolute,|,styleprops,|,cite,abbr,acronym,del,ins,attribs,|,visualchars,nonbreaking",
theme_advanced_toolbar_location : "top",
theme_advanced_toolbar_align : "left",
theme_advanced_path_location : "bottom",
extended_valid_elements : "a[name|href|target|title|onclick],img[class|src|border=0|alt|title|hspace|vspace|width|height|align|onmouseover|onmouseout|name],hr[class|width|size|noshade],font[face|size|color|style],span[class|align|style]",
theme_advanced_resize_horizontal : true,
theme_advanced_resizing : true,
apply_source_formatting : true,
//the following removes font tags and replaces with span tags for accessibility
convert_fonts_to_spans : true,
font_size_classes : "fontSize1,fontSize2,fontSize3,fontSize4,fontSize5,fontSize6,fontSize7",
font_size_style_values : "xx-small,x-small,small,medium,large,x-large,xx-large",
//end font to span tags section
content_css : "/styles/custom.css",
relative_urls : false,
editor_selector : "mceEditor"
});
//-->
.