So there's Philip V, king of France, and his wife Joan of Burgundy, and his first cousin Philip VI, king of France, and his wife Joan of Burgundy. Another Joan of Burgundy. So no, that's not confusing at all. There was a county of Burgundy, also known as the Franche-Comté, and a duchy of Burgundy, which shared a border but were not the same place. Also not at all confusing.
Joan of Burgundy, queen of Philip V (the second of the three brothers of Edward II's queen Isabella) was the elder of the two daughters of Othon IV, count of Burgundy, and Mahaut, countess of Artois in her own right. Joan was born in about 1287 or 1288, according to historian Elizabeth A. R. Brown, an expert on the French royal family of this period (Joan's Wiki page gives her date of birth as 15 January 1292, but I have no idea where that comes from). Mahaut, a major character in Maurice Druon's series of novels The Accursed Kings, was born in 1268 or 1269, and inherited her father Robert's county of Artois in preference to her brother Philip's son Robert of Artois (born 1287). Mahaut was the niece of Blanche of Artois, queen of Navarre and countess of Lancaster, the maternal grandmother of Philip V, which makes Philip and Joan of Burgundy second cousins. The couple married in 1307. Joan had a younger sister Blanche, born in 1295 or 1296, who married Philip V's younger brother Charles in January 1308, the week before their sister Isabella married Edward II. Joan and Blanche also had a brother, Robert of Burgundy, who died unmarried and childless in 1317 (his future marriage to Edward I's youngest child Eleanor had been proposed shortly after her birth in May 1306). As the elder sister, Joan inherited Burgundy from Robert and ultimately from their father Othon (died 1302), and inherited Artois as well when Mahaut died in 1329. Blanche of Burgundy was imprisoned for adultery in 1314, her marriage was annulled in 1322, and she died in late 1325 or early 1326, still only thirty.
Philip V's elder brother Louis X was born on 4 October 1289 and his younger brother Charles IV on 18 June 1294, but his own date of birth is not known. He was said to be thirty when he died at the beginning of 1322, which would place it sometime in 1291. Philip was thus some years younger than his wife Joan. Their eldest child, another Joan, was born in 1308 when Philip was still only a teenager. Joan of France later inherited the counties of Burgundy and Artois from her mother, and was also duchess of Burgundy by marriage to Odo IV (see also below). Philip V and Joan of Burgundy's other daughters were Marguerite, countess of Flanders, Isabella, dauphine of Vienne, and Blanche, a nun; their two sons Philip and Louis died young. Philip V was thus succeeded by his brother Charles IV when he died at the age of only thirty, having been king of France for only five years. His widow Joan of Burgundy also died at a fairly young age, in January 1330, only a few weeks after her mother Mahaut.
The other Joan of Burgundy married Philip of Valois, the future Philip VI of France (who succeeded his first cousin Charles IV in 1328 when Charles also died without sons) in July 1313. Joan and Philip were first cousins once removed: she was the granddaughter of Saint Louis IX of France and Marguerite of Provence, Philip their great-grandson. Joan was the third daughter of Louis IX's youngest child Agnes of France (c. 1260-1327) and Duke Robert II of Burgundy, and was born in about 1293, the same year as her husband; her siblings included Duke Hugh V, Duke Odo IV (who married Philip V and the other Joan of Burgundy's eldest daughter, as above), and Marguerite, who married Louis X of France as his first wife and was imprisoned for adultery in 1314. Marguerite was the mother of Queen Joan II of Navarre.
This Joan of Burgundy was apparently lame, and grossly unpopular: she was known as la male royne boiteuse, 'the evil lame queen'. She was the mother of King John II of France, born in 1319, and Philip, duke of Orleans, who married Charles IV's posthumous daughter Blanche of France, his only child who lived into adulthood. Joan died in 1348, and her widower Philip VI married the forty years younger Blanche of Navarre, also sometimes known as Blanche of Evreux, who was the daughter of Queen Joan II of Navarre and who, like Joan of Burgundy, was Philip's first cousin once removed. Blanche of Navarre/Evreux's parents Joan II of Navarre and Philip of Evreux were first cousins once removed. The parents of Blanche of France, duchess of Orleans - Charles IV and Joan of Evreux - were first cousins. Joan of Evreux was the sister of Philip of Evreux, who married Joan II of Navarre and was the father-in-law of Philip VI. Charles IV's daughter Blanche of France and her husband Philip, duke of Orleans were second cousins. Louis X of France and his wife Marguerite of Burgundy were first cousins once removed, and Philip VI and his wife Joan of Burgundy, Marguerite's sister, were also first cousins once removed. Philip IV of France and his wife Joan I of Navarre, parents of Louis X, Philip V, Charles IV and Edward II's queen Isabella, were second cousins. Charles II 'the Bad', king of Navarre, son of Joan II of Navarre and Philip of Evreux, married Joan of France, daughter of King John II and granddaughter of Philip VI and Joan of Burgundy: they were second cousins. These people were so interrelated, it makes my brain explode.
All three sons of Philip IV of France, and his nephew Philip VI, married women of Burgundy. Saint Louis IX of France's youngest son, Robert, count of Clermont, Agnes of France's brother and thus the uncle of Philip VI's wife Joan of Burgundy (and the great-uncle of Louis X and his brothers and Philip VI), also married a woman of Burgundy. She was Beatrice of Burgundy, the heiress of Bourbon, a first cousin of Joan of Burgundy who married Philip VI and of Marguerite of Burgundy who married Louis X: all of them were grandchildren of Duke Hugh IV of Burgundy. My brain actually exploded at that point.