Explorer Replacement won't work if Opus has been launched elevated (Administrator), which may explain why you see the problem sometimes but not others.
If the process is elevated it should say "ADMINISTRATOR:" in all caps in the window title. Avoid that, and instead use the Admin Mode / UAC support built into Opus (which will put "Administrator:" in the title instead.) See Why NOT to run Opus as Administrator under UAC for more detail.
Other than that, I don't know of a reason why double-clicks on the same folder, from the same program (e.g. the Windows desktop) would work sometimes but not others, unless the machine was under really heavy load and the Explorer Replacement check was timing out.