I have a test where one command is a "waitForCondition" with a timeout of 50ms. Then a few commands later, I call the "open" command. That command will abort with a timeout exception after 50ms.

I hacked the following patch:
--- core/scripts/selenium-executionloop.js (revision 10102)
+++ core/scripts/selenium-executionloop.js (working copy)
@@ -110,6 +110,7 @@
         this.commandComplete(result);
 
if (result.processState == SELENIUM_PROCESS_WAIT) {
+ this.waitForConditionTimeout = 30 * 1000;
             this.waitForCondition = function() {
                 LOG.debug("Checking condition: isNewPageLoaded?");
                 return selenium.browserbot.isNewPageLoaded();

But that's probably not the clean solution.