When you start using flash modifiers (like diffusers) on an E-TTL flash head like a Speedlite then you are getting into situations where the E-TTL system is far less likely to successfully automatically compensate like it can using its build in "wide screen" and/or other built in flash modifiers that signal the system what changes have been made. A diffuser is generally going to "eat" at least one full stop of light and many will cause an even greater decrease so it will be very noticeable and as you change the pattern of light dispersal then your choice of metering setup on the camera also becomes more critical. With a light modifier, the flash isn't producing the amount of usable illumination that the camera expects when it commands a specific flash power setting and the diffuser also largely defeats the functionality of the flash "zoom" compensation by broadening the narrowed light beam the flash tries to produce thus the bigger issue with the lens zoomed to more extreme focal length.
You could try dialing in exposure compensation but since you already have the camera in manual mode I would also put your Speedlite in manual mode so that you have full direct control over all of the exposure variables. This is a case where an external light meter can take a LOT of wasted time and frustration out of the process. You don't need an expensive complex meter and an under $200 meter from one of the established providers will serve you well for a very long time.
Also keep in mind that as you reduce the light output of the Speedlite via a diffuser, its power level has to be increased to compensate and this can get you into heating issues very quickly that are exacerbated by a diffuser that further reduces cooling of the Speedlite. Smaller hot shoe mounted flashes are very useful but forcing them to produce a continued series of full power flashes will stress the system rapidly. Unlike larger studio flashes which have forced air cooling to keep the xenon flash tube, transistor inverter supply, and capacitor bank cool a Speedlite is largely sealed to protect it from dirt and moisture but this impedes cooling. Using it at maximum power with a diffuser in place means you should keep in mind that the minimum recycle time it can provide with its external battery pack doesn't mean it is a good idea to fire it at a high duty cycle with very short periods in between flashes. This is another case where the light meter is nearly worth its weight in gold because it allows you to quickly dial in the correct flash power and camera "exposure triangle" settings instead of the test fire and review approach.
Since forum rules will strip most links, do a search for: Gossen exposure metering compendium PDF. Gossen is an old line German manufacturer of light meters among other products and their compendium will provide you with one of the best written and easiest to understand explanation of photographic exposure and lighting that you will find anywhere. It is a free download and one of those rare cases where some highly technical subject matter is presented in an extremely understandable manner.
Rodger
EOS 1DX M3, 1DX M2, 1DX, 5DS R, M6 Mark II, 1D M2, EOS 650 (film), many lenses, XF400 video
