Appium: Waiting for elements on iOS doesn't work anymore - ios

Question

I'm automizing tests for Android and iOS. Lately (probably after I've updated to appium 1.9.1 and java-client 6.1.0) I have issues with the iOS tests.
Many tests fail, because WebElements couldn't be found. I'm using WebDriverWait to find elements like in this example:
private WebElement getWebElement(By by, int timeOutInSeconds) {
return (new WebDriverWait(appiumDriver, timeOutInSeconds)).until(ExpectedConditions.presenceOfElementLocated(by));
}
The tests don't wait to find the element anymore. Instead an exception is thrown immediately.
I'm using XCUITest for iOS and uiautomator2 on android. On android the tests are still fine.
Edit (2018-10-29 18:33):
It feels like page factory is reporting the element is there, then randomElement.isDisplayed() will be executed on the element which throws directly an error, because it can't find the element.
And another observation:
In some cases the waiting duration works properly on iOS, but I couldn't find a pattern yet.
Edit (2018-12-14 15:56):
Still no solution found. Note: My tests make screenshots on failure. I can see on a lot of screenshots, the elements that caused the failure. The logs say they couldn't be found, but I can clearly see them on the screen. Makes no sense. Hoping for ideas!
Edit (2019-01-11 15:05):
In the logs, it looks like the element is found (response 200), but when I want to perform a click, it says it's 'not visible on the screen an thus not interactable'.
...
[HTTP] --> POST /wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/element
[HTTP] {"using":"id","value":"myapp"}
[debug] [W3C] Calling AppiumDriver.findElement() with args: ["id","buttonNext","59e9ace4-55a5-4b07-ad0e-af874dc42a6d"]
[debug] [XCUITest] Executing command 'findElement'
[debug] [BaseDriver] Valid locator strategies for this request: xpath, id, name, class name, -ios predicate string, -ios class chain, accessibility id
[debug] [BaseDriver] Waiting up to 0 ms for condition
[debug] [JSONWP Proxy] Matched '/element' to command name 'findElement'
[debug] [JSONWP Proxy] Proxying [POST /element] to [POST http://localhost:8100/session/CE691ADA-FC54-48AE-9AA0-1DA6212DB2CC/element] with body: {"using":"id","value":"buttonNext"}
[debug] [JSONWP Proxy] Got response with status 200: {"value":{"ELEMENT":"24010000-0000-0000-0308-000000000000"},"sessionId":"CE691ADA-FC54-48AE-9AA0-1DA6212DB2CC","status":0}
[debug] [W3C] Responding to client with driver.findElement() result: {"element-6066-11e4-a52e-4f735466cecf":"24010000-0000-0000-0308-000000000000"}
[HTTP] <-- POST /wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/element 200 180 ms - 88
[HTTP]
[HTTP] --> POST /wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/element/24010000-0000-0000-0308-000000000000/click
[HTTP] {"id":"24010000-0000-0000-0308-000000000000"}
[W3C] Driver proxy active, passing request on via HTTP proxy
[debug] [XCUITest] Executing command 'proxyReqRes'
[debug] [JSONWP Proxy] Matched '/wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/element/24010000-0000-0000-0308-000000000000/click' to command name 'click'
[debug] [JSONWP Proxy] Proxying [POST /wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/element/24010000-0000-0000-0308-000000000000/click] to [POST http://localhost:8100/session/CE691ADA-FC54-48AE-9AA0-1DA6212DB2CC/element/24010000-0000-0000-0308-000000000000/click] with body: {"id":"24010000-0000-0000-0308-000000000000"}
[debug] [JSONWP Proxy] Got response with status 200: {"value":"Error Domain=com.facebook.WebDriverAgent Code=1 \"The element '\"buttonNext\" Button' is not visible on the screen and thus is not interactable\" UserInfo={NSLocalizedDescription=The element '\"buttonNext\" Button' is not visible on the screen and thus is not interactable}","sessionId":"CE691ADA-FC54-48AE-9AA0-1DA6212DB2CC","status":13}
[debug] [W3C] Encountered internal error running command: ProxyRequestError: Could not proxy command to remote server. Original error: The request to /wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/element/24010000-0000-0000-0308-000000000000/click has failed
[debug] [W3C] at JWProxy.proxy$ (/usr/local/lib/node_modules/appium/node_modules/appium-base-driver/lib/jsonwp-proxy/proxy.js:182:13)
[debug] [W3C] at tryCatch (/usr/local/lib/node_modules/appium/node_modules/babel-runtime/regenerator/runtime.js:67:40)
[debug] [W3C] at GeneratorFunctionPrototype.invoke [as _invoke] (/usr/local/lib/node_modules/appium/node_modules/babel-runtime/regenerator/runtime.js:315:22)
[debug] [W3C] at GeneratorFunctionPrototype.prototype.(anonymous function) [as next] (/usr/local/lib/node_modules/appium/node_modules/babel-runtime/regenerator/runtime.js:100:21)
[debug] [W3C] at GeneratorFunctionPrototype.invoke (/usr/local/lib/node_modules/appium/node_modules/babel-runtime/regenerator/runtime.js:136:37)
[debug] [MJSONWP] Matched JSONWP error code 13 to UnknownError
[HTTP] <-- POST /wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/element/24010000-0000-0000-0308-000000000000/click 500 4875 ms - 1779
[HTTP]
[HTTP] --> GET /wd/hub/session/59e9ace4-55a5-4b07-ad0e-af874dc42a6d/screenshot
[HTTP] {}
...