Are there conventions for research paper flowcharts?

The answer to this question is actually not specific to research.

There is an ISO Norm on flowcharts that describes the basic elements and what the shapes represent. This is norm ISO 5807:1985.

The bad thing about ISO norms is that you can't simply download them free of charge. But the good news is that in academia, unless you are doing research on flow charts themselves, nobody will care if you do not adhere to the standard in the strictest possible way. The Wikipedia page on flow-charts is a good starting point, and a search on flowchart elements also seems to lead to some useful sites. Also, looking at the set of predefined shapes in drawing software that is also meant to be used for flow-charting (e.g., Microsoft Visio) gives you a good idea of what elements there are and what they represent.

Apart from the symbol concessions pointed out by @DCTLib, the uniformity of the flowchart is indeed important.

• Same font size for all labels
• Neat spacing between symbols
• Same set of colours (if any). But sticking to black or light blue might seem more professional.

You may use a set of symbols that best describe your method, but make sure that you mean the same the throughout.

E.g., don't use both rectangles and rounded rectangles to denote processes in the same paper/presentation.