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In general, the PLS algorithm is identical and the results should not differ. The reason of unlike results is the selection different settings.
You must choose identical settings when starting the algorithm in SmartPLS 2 and SmartPLS 3. When using the same settings, SmartPLS 2 and SmartPLS 3 return the same PLS-SEM results, as shown below.
Especially when you import a SmartPLS 2 project into SmartPLS 3, some settings are not transferred and you have to make sure to set them up accordingly in SmartPLS 3. You need to check 2 things:
Open the data view for your CSV file in SmartPLS 3 and indicate the missing value if there is one. Otherwise your missing value (e.g. -99) will be interpreted as normal data which will falsify your results.
Check the data format that is set up for your CSV file. If the wrong format (e.g. Europe instead of US) is used, all of your values are interpreted wrong. Please note that you can also setup a default number format in the preferences (-> Edit -> Preferences -> Number Format).